[[File:Richard Linderum Der Blumenfreund.jpg|thumb|300px|Alt=Image of ripe nutmeg fruit split open to show red aril|The fruit of ''[[Myristica fragrans]]'', a species native to [[Indonesia]], is the source of two valuable spices, the red aril ([[mace (spice)|mace]]) enclosing the dark brown [[nutmeg]].]]

{{Good article}}{{Use British English|date=September 2016}}

'''Botany''', also called '''plant science'''('''s'''), '''plant biology''' or '''phytology''', is the science of [[plant]] life and a branch of [[biology]]. A '''botanist''' or '''plant scientist''' is a [[scientist]] who specialises in this field. The term "botany" comes from the [[Ancient Greek]] word {{lang|grc|βοτάνη}} (''botanē'') meaning "[[pasture]]", "grass", or "[[fodder]]"; {{lang|grc|βοτάνη}} is in turn derived from {{lang|grc|βόσκειν}} (''boskein''), "to feed" or "to graze".{{sfn|Liddell|Scott|1940}}{{sfn|Gordh|Headrick|2001|p = 134}}{{sfn|Online Etymology Dictionary|2012}} Traditionally, botany has also included the study of [[Fungus|fungi]] and [[algae]] by [[mycologist]]s and [[phycologist]]s respectively, with the study of these three groups of organisms remaining within the sphere of interest of the [[International Botanical Congress]]. Nowadays, botanists (in the strict sense) study approximately 410,000 [[species]] of [[Embryophyte|land plants]] of which some 391,000 species are [[vascular plant]]s (including ca 369,000 species of [[flowering plant]]s),<ref>RBG Kew (2016). The State of the World’s Plants Report – 2016. Royal Botanic Gardens, Kew. https://stateoftheworldsplants.com/report/sotwp_2016.pdf</ref> and ca 20,000 are [[bryophyte]]s.<ref>{{Cite web|url=http://www.theplantlist.org/1.1/browse/B/|title=The Plant List - Bryophytes|last=|first=|date=|website=|dead-url=|access-date=}}</ref>

Botany originated in prehistory as [[herbalism]] with the efforts of early humans to identify – and later cultivate – edible, medicinal and poisonous plants, making it one of the oldest branches of science. Medieval [[physic garden]]s, often attached to monasteries, contained plants of medical importance. They were forerunners of the first [[botanical garden]]s attached to universities, founded from the 1540s onwards. One of the earliest was the [[Orto botanico di Padova|Padua botanical garden]]. These gardens facilitated the academic study of plants. Efforts to catalogue and describe their collections were the beginnings of [[plant taxonomy]], and led in 1753 to the [[binomial nomenclature|binomial system]] of [[Carl Linnaeus]] that remains in use to this day.

In the 19th and 20th centuries, new techniques were developed for the study of plants, including methods of [[optical microscope|optical microscopy]] and [[live cell imaging]], [[electron microscopy]], analysis of [[ploidy|chromosome number]], [[phytochemistry|plant chemistry]] and the structure and function of [[enzyme]]s and other [[protein]]s. In the last two decades of the 20th century, botanists exploited the techniques of [[molecular biology|molecular genetic analysis]], including [[genomics]] and [[proteomics]] and [[DNA sequences]] to classify plants more accurately.

Modern botany is a broad, multidisciplinary subject with inputs from most other areas of science and technology. Research topics include the study of plant [[Plant morphology|structure]], [[cell growth|growth]] and differentiation, [[Plant reproduction|reproduction]], [[plant physiology#Biochemistry of plants|biochemistry]] and [[metabolism|primary metabolism]], [[phytochemistry|chemical products]], [[Plant morphology#Development|development]], [[plant pathology|diseases]], [[phylogenetics|evolutionary relationships]], systematics, and [[Taxonomy (biology)|plant taxonomy]]. Dominant themes in 21st century plant science are [[molecular genetics]] and [[epigenetics]], which are the mechanisms and control of gene expression during differentiation of [[plant cell]]s and [[Tissue (biology)#Plant tissues|tissues]]. Botanical research has diverse applications in providing [[staple foods]], materials such as timber, oil, rubber, fibre and drugs, in modern horticulture, agriculture and [[forestry]], [[plant propagation]], [[Plant breeding|breeding]] and [[genetic modification]], in the synthesis of chemicals and raw materials for construction and energy production, in [[environmental management]], and the maintenance of [[biodiversity]].

== History ==

{{Main article|History of botany}}

=== Early botany ===

[[File:Cork Micrographia Hooke.png|thumb|Alt=engraving of cork cells from Hooke's Micrographia, 1665|An engraving of the cells of [[Cork oak|cork]], from [[Robert Hooke]]'s ''[[Micrographia]]'', 1665]]

Botany originated as [[herbalism]], the study and use of plants for their medicinal properties.{{sfn|Sumner|2000|p = 16}} Many records of the [[Holocene]] period date early botanical knowledge as far back as 10,000 years ago.<ref name=":0">{{Cite journal|last=Delcourt|first=Paul A.|last2=Delcourt|first2=Hazel R.|last3=Cridlebaugh|first3=Patricia A.|last4=Chapman|first4=Jefferson|date=1986-05-01|title=Holocene ethnobotanical and paleoecological record of human impact on vegetation in the Little Tennessee River Valley, Tennessee|url=http://www.sciencedirect.com/science/article/pii/0033589486900050|journal=Quaternary Research|volume=25|issue=3|pages=330–349|doi=10.1016/0033-5894(86)90005-0|bibcode=1986QuRes..25..330D}}</ref> This early unrecorded knowledge of plants was discovered in ancient sites of human occupation within [[Tennessee]], which make up much of the [[Cherokee]] land today.<ref name=":0" /> The early recorded history of botany includes many ancient writings and plant classifications. Examples of early botanical works have been found in ancient texts from India dating back to before 1100 BC,{{sfn|Reed|1942|pp = 7–29}}{{sfn|Oberlies|1998|p = 155}} in archaic [[Avestan language|Avestan]] writings, and in works from China before it was unified in 221 BC.{{sfn|Reed|1942|pp = 7–29}}{{sfn|Needham|Lu|Huang|1986}}

Modern botany traces its roots back to [[Ancient Greece]] specifically to [[Theophrastus]] (c. 371–287 BC), a student of [[Aristotle]] who invented and described many of its principles and is widely regarded in the [[scientific community]] as the "Father of Botany".{{sfn|Greene|1909|pp = 140–142}} His major works, ''[[Historia Plantarum (Theophrastus)|Enquiry into Plants]]'' and ''On the Causes of Plants'', constitute the most important contributions to botanical science until the [[Middle Ages]], almost seventeen centuries later.{{sfn|Greene|1909|pp = 140–142}}{{sfn|Bennett|Hammond|1902|p = 30}}

Another work from Ancient Greece that made an early impact on botany is ''De Materia Medica'', a five-volume encyclopedia about [[Herbalism|herbal medicine]] written in the middle of the first century by Greek physician and pharmacologist [[Pedanius Dioscorides]]. ''De Materia Medica'' was widely read for more than 1,500 years.{{sfn|Mauseth|2003|p = 532}} Important contributions from the [[Islamic Golden Age|medieval Muslim world]] include [[Ibn Wahshiyya]]'s ''Nabatean Agriculture'', [[Abū Ḥanīfa Dīnawarī]]'s (828–896) the ''Book of Plants'', and [[Ibn Bassal]]'s ''The Classification of Soils''. In the early 13th century, Abu al-Abbas al-Nabati, and [[Ibn al-Baitar]] (d. 1248) wrote on botany in a systematic and scientific manner.{{sfn|Dallal|2010|p = 197}}{{sfn|Panaino|2002|p = 93}}{{sfn|Levey|1973|p = 116}}

In the mid-16th century, "[[botanical garden]]s" were founded in a number of Italian universities – the [[Orto botanico di Padova|Padua botanical garden]] in 1545 is usually considered to be the first which is still in its original location. These gardens continued the practical value of earlier "physic gardens", often associated with monasteries, in which plants were cultivated for medical use. They supported the growth of botany as an academic subject. Lectures were given about the plants grown in the gardens and their medical uses demonstrated. Botanical gardens came much later to northern Europe; the first in England was the [[University of Oxford Botanic Garden]] in 1621. Throughout this period, botany remained firmly subordinate to medicine.{{sfn|Hill|1915}}

German physician [[Leonhart Fuchs]] (1501–1566) was one of "the three German fathers of botany", along with theologian [[Otto Brunfels]] (1489–1534) and physician [[Hieronymus Bock]] (1498–1554) (also called Hieronymus Tragus).{{sfn|National Museum of Wales|2007}}{{sfn|Yaniv|Bachrach|2005|p = 157}} Fuchs and Brunfels broke away from the tradition of copying earlier works to make original observations of their own. Bock created his own system of plant classification.

Physician [[Valerius Cordus]] (1515–1544) authored a botanically and pharmacologically important herbal ''Historia Plantarum'' in 1544 and a [[pharmacopoeia]] of lasting importance, the ''Dispensatorium'' in 1546.{{sfn|Sprague|1939}} Naturalist [[Conrad von Gesner]] (1516–1565) and herbalist [[John Gerard]] (1545–c. 1611) published herbals covering the medicinal uses of plants. Naturalist [[Ulisse Aldrovandi]] (1522–1605) was considered the ''father of natural history'', which included the study of plants. In 1665, using an early microscope, [[Polymath]] [[Robert Hooke]] discovered [[cell (biology)|cells]], a term he coined, in [[cork (material)|cork]], and a short time later in living plant tissue.{{sfn|Waggoner|2001}}

=== Early modern botany ===

{{Further information|Taxonomy (biology)#History of taxonomy}}

[[File:CarlvonLinne Garden.jpg|thumb|left|Alt=Photograph of a garden|The [[Linnaean Garden]] of Linnaeus' residence in Uppsala, Sweden, was planted according to his ''Systema sexuale''.]]

During the 18th century, systems of [[plant identification]] were developed comparable to [[single access key|dichotomous keys]], where unidentified plants are placed into [[taxon]]omic groups (e.g. family, genus and species) by making a series of choices between pairs of [[Character (biology)|characters]]. The choice and sequence of the characters may be artificial in keys designed purely for identification ([[single access key#Diagnostic ('artificial') versus synoptic ('natural') keys|diagnostic keys]]) or more closely related to the natural or [[taxonomic order|phyletic order]] of the [[taxon|taxa]] in synoptic keys.{{sfn|Scharf|2009|pp = 73–117}} By the 18th century, new plants for study were arriving in Europe in increasing numbers from newly discovered countries and the European colonies worldwide. In 1753 [[Carl Linnaeus|Carl von Linné]] (Carl Linnaeus) published his [[Species Plantarum]], a hierarchical classification of plant species that remains the reference point for [[International Code of Nomenclature for algae, fungi, and plants|modern botanical nomenclature]]. This established a standardised binomial or two-part naming scheme where the first name represented the [[genus]] and the second identified the [[species]] within the genus.{{sfn|Capon|2005|pp = 220–223}} For the purposes of identification, Linnaeus's ''Systema Sexuale'' [[Linnaean taxonomy#Classification for plants|classified]] plants into 24 groups according to the number of their male sexual organs. The 24th group, ''Cryptogamia'', included all plants with concealed reproductive parts, mosses, liverworts, ferns, algae and fungi.{{sfn|Hoek|Mann|Jahns|2005|p = 9}}

Increasing knowledge of [[plant anatomy]], [[plant morphology|morphology]] and life cycles led to the realisation that there were more natural affinities between plants than the artificial sexual system of Linnaeus. [[Michel Adanson|Adanson]] (1763), [[Antoine Laurent de Jussieu|de Jussieu]] (1789), and [[Augustin Pyramus de Candolle|Candolle]] (1819) all proposed various alternative natural systems of classification that grouped plants using a wider range of shared characters and were widely followed. The [[Candollean system]] reflected his ideas of the progression of morphological complexity and the [[Bentham & Hooker system|later classification]] by [[George Bentham|Bentham]] and [[J.D. Hooker|Hooker]], which was influential until the mid-19th century, was influenced by Candolle's approach. [[Charles Darwin|Darwin]]'s publication of the ''[[On the Origin of Species|Origin of Species]]'' in 1859 and his concept of common descent required modifications to the Candollean system to reflect evolutionary relationships as distinct from mere morphological similarity.{{sfn|Starr|2009|p =299–}}

Botany was greatly stimulated by the appearance of the first "modern" textbook, [[Matthias Jakob Schleiden|Matthias Schleiden]]'s ''{{lang|de|Grundzüge der Wissenschaftlichen Botanik}}'', published in English in 1849 as ''Principles of Scientific Botany''.{{sfn|Morton|1981|p = 377}} Schleiden was a microscopist and an early plant anatomist who co-founded the [[cell theory]] with [[Theodor Schwann]] and [[Rudolf Virchow]] and was among the first to grasp the significance of the [[cell nucleus]] that had been described by [[Robert Brown (botanist, born 1773)|Robert Brown]] in 1831.{{sfn|Harris|2000|pp = 76–81}}

In 1855, [[Adolf Fick]] formulated [[Fick's laws of diffusion|Fick's laws]] that enabled the calculation of the rates of [[molecular diffusion]] in biological systems.{{sfn|Small|2012|p =118–}}

[[File:Echeveria glauca II.jpg|thumb|''Echeveria glauca'' in a Connecticut greenhouse. Botany uses Latin names for identification, here, the specific name ''glauca'' means blue.]]

=== Modern botany ===

[[File:Apfe-auf-Naehrboden.jpg|thumb|200px|Alt=Micropropagation of transgenic plants|Micropropagation of transgenic plants]]

Building upon the gene-chromosome theory of heredity that originated with [[Gregor Mendel]] (1822–1884), [[August Weismann]] (1834–1914) proved that inheritance only takes place through [[gamete]]s. No other cells can pass on inherited characters.{{sfn|Karp|2009|p = 382}} The work of [[Katherine Esau]] (1898–1997) on plant anatomy is still a major foundation of modern botany. Her books ''Plant Anatomy'' and ''Anatomy of Seed Plants'' have been key plant structural biology texts for more than half a century.{{sfn|National Science Foundation|1989}}{{sfn|Chaffey|2007|pp = 481–482}}

The discipline of [[plant ecology]] was pioneered in the late 19th century by botanists such as [[Eugenius Warming]], who produced the hypothesis that plants form [[plant community|communities]], and his mentor and successor [[Christen C. Raunkiær]] whose system for describing [[Raunkiær plant life-form|plant life forms]] is still in use today. The concept that the composition of plant communities such as [[Temperate broadleaf and mixed forests|temperate broadleaf forest]] changes by a process of [[ecological succession]] was developed by [[Henry Chandler Cowles]], [[Arthur Tansley]] and [[Frederic Clements]]. Clements is credited with the idea of [[climax vegetation]] as the most complex vegetation that an environment can support and Tansley introduced the concept of [[ecosystem]]s to biology.{{sfn|Tansley|1935|pp=299–302}}{{sfn|Willis|1997||pp=267–271}}{{sfn|Morton|1981|p = 457}} Building on the extensive earlier work of [[Alphonse Pyramus de Candolle|Alphonse de Candolle]], [[Nikolai Ivanovich Vavilov|Nikolai Vavilov]] (1887–1943) produced accounts of the [[biogeography]], [[Center of origin|centres of origin]], and evolutionary history of economic plants.{{sfn|de Candolle|2006|pp = 9–25, 450–465}}

Particularly since the mid-1960s there have been advances in understanding of the physics of [[Plant physiology|plant physiological]] processes such as [[transpiration]] (the transport of water within plant tissues), the temperature dependence of rates of water [[evaporation]] from the leaf surface and the [[molecular diffusion]] of water vapour and carbon dioxide through [[stomatal]] apertures. These developments, coupled with new methods for measuring the size of stomatal apertures, and the rate of [[photosynthesis]] have enabled precise description of the rates of [[gas exchange]] between plants and the atmosphere.{{sfn|Jasechko|Sharp|Gibson|Birks|2013|pp = 347–350}}{{sfn|Nobel|1983|p = 608}} Innovations in [[Statistics|statistical analysis]] by [[Ronald Fisher]],{{sfn|Yates|Mather|1963|pp = 91–129}} [[Frank Yates]] and others at [[Rothamsted Research#Statistical science|Rothamsted Experimental Station]] facilitated rational experimental design and data analysis in botanical research.{{sfn|Finney|1995|pp = 554–573}} The discovery and identification of the [[auxin]] [[Plant physiology#Plant hormones|plant hormones]] by [[Kenneth V. Thimann]] in 1948 enabled regulation of plant growth by externally applied chemicals. [[Frederick Campion Steward]] pioneered techniques of [[micropropagation]] and [[plant tissue culture]] controlled by plant hormones.{{sfn|Cocking|1993}} The synthetic auxin [[2,4-Dichlorophenoxyacetic acid]] or 2,4-D was one of the first commercial synthetic herbicides.{{sfn|Cousens|Mortimer|1995}}

20th century developments in plant biochemistry have been driven by modern techniques of [[organic chemistry|organic chemical analysis]], such as [[spectroscopy]], [[chromatography]] and [[electrophoresis]]. With the rise of the related molecular-scale biological approaches of [[molecular biology]], [[genomics]], [[proteomics]] and [[metabolomics]], the relationship between the plant [[genome]] and most aspects of the biochemistry, physiology, morphology and behaviour of plants can be subjected to detailed experimental analysis.{{sfn|Ehrhardt|Frommer|2012|pp = 1–21}} The concept originally stated by [[Gottlieb Haberlandt]] in 1902{{sfn|Haberlandt|1902|pages=69–92}} that all plant cells are [[Cell potency#Totipotency|totipotent]] and can be grown ''in vitro'' ultimately enabled the use of [[genetic engineering]] experimentally to knock out a gene or genes responsible for a specific trait, or to add genes such as [[Green fluorescent protein|GFP]] that [[reporter gene|report]] when a gene of interest is being expressed. These technologies enable the biotechnological use of whole plants or plant cell cultures grown in [[bioreactors]] to synthesise [[Bt corn|pesticides]], [[Biopharmaceutics|antibiotics]] or other [[pharming (genetics)|pharmaceuticals]], as well as the practical application of [[genetically modified crops]] designed for traits such as improved yield.{{sfn|Leonelli|Charnley|Webb|Bastow|2012}}

Modern morphology recognises a continuum between the major morphological categories of root, stem (caulome), leaf (phyllome) and trichome.{{sfn|Sattler|Jeune|1992|pp = 249-262}} Furthermore, it emphasises structural dynamics.{{sfn|Sattler|1992|pp = 708-714}} Modern systematics aims to reflect and discover [[Phylogenetic nomenclature|phylogenetic relationships]] between plants.{{sfn|Ereshefsky|1997|pp = 493–519}}{{sfn|Gray|Sargent|1889|pp = 292–293}}{{sfn|Medbury|1993|pp = 14–16}}{{sfn|Judd|Campbell|Kellogg|Stevens|2002|pp = 347–350}} Modern [[Molecular phylogenetics]] largely ignores morphological characters, relying on DNA sequences as data. Molecular analysis of [[nucleic acid sequence|DNA sequences]] from most families of flowering plants enabled the [[Angiosperm Phylogeny Group]] to publish in 1998 a [[phylogenetics|phylogeny]] of flowering plants, answering many of the questions about relationships among [[angiosperm]] families and species.{{sfn|Burger|2013}} The theoretical possibility of a practical method for identification of plant species and commercial varieties by [[DNA barcoding]] is the subject of active current research.{{sfn|Kress|Wurdack|Zimmer|Weigt|2005|pp = 8369–8374}}{{sfn|Janzen|Forrest|Spouge|Hajibabaei|2009|pp = 12794–12797}}

== Scope and importance ==

[[File:Neuchâtel Herbarium - Athyrium filix-femina - NEU000003080.tif|left|thumb|Alt=A herbarium specimen of the lady fern, ''Athyrium filix-femina''|Botany involves the recording and description of plants, such as this herbarium specimen of the lady fern ''[[Athyrium filix-femina]]''.]]

The study of plants is vital because they underpin almost all animal life on Earth by generating a large proportion of the [[oxygen]] and food that provide humans and other organisms with [[cellular respiration|aerobic respiration]] with the chemical energy they need to exist. Plants, [[algae]] and [[cyanobacteria]] are the major groups of organisms that carry out [[photosynthesis]], a process that uses the energy of sunlight to convert water and [[carbon dioxide]]{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 186–187}} into sugars that can be used both as a source of chemical energy and of organic molecules that are used in the structural components of cells.{{sfn|Campbell|Reece|Urry|Cain|2008|p = 1240}} As a by-product of photosynthesis, plants release [[oxygen]] into the atmosphere, a gas that is required by [[anaerobic organism|nearly]] all living things to carry out cellular respiration. In addition, they are influential in the global [[carbon cycle|carbon]] and [[water cycle|water]] cycles and plant roots bind and stabilise soils, preventing soil [[erosion]].{{sfn|Gust|1996}} Plants are crucial to the future of human society as they provide food, oxygen, medicine, and products for people, as well as creating and preserving soil.{{sfn|Missouri Botanical Garden|2009}}

Historically, all living things were classified as either animals or plants{{sfn|Chapman et al.|2001|p = 56}} and botany covered the study of all organisms not considered animals.{{sfn|Braselton|2013}} Botanists examine both the internal functions and processes within plant [[organelle]]s, cells, tissues, whole plants, plant populations and plant communities. At each of these levels, a botanist may be concerned with the classification ([[Taxonomy (biology)|taxonomy]]), [[phylogeny]] and [[evolution]], structure ([[Plant anatomy|anatomy]] and [[Plant morphology|morphology]]), or function ([[Plant physiology|physiology]]) of plant life.{{sfn|Ben-Menahem|2009|p = 5368}}

The strictest definition of "plant" includes only the "land plants" or [[embryophytes]], which include [[seed plants]] (gymnosperms, including the [[Pinophyta|pines]], and [[flowering plant]]s) and the free-sporing [[cryptogams]] including [[fern]]s, [[Lycopodiopsida|clubmosses]], [[Marchantiophyta|liverworts]], [[hornwort]]s and [[moss]]es. Embryophytes are multicellular [[eukaryote]]s descended from an ancestor that obtained its energy from sunlight by [[photosynthesis]]. They have life cycles with [[alternation of generations|alternating]] [[haploid]] and [[diploid]] phases. The sexual haploid phase of embryophytes, known as the [[gametophyte]], nurtures the developing diploid embryo [[sporophyte]] within its tissues for at least part of its life,{{sfn|Campbell|Reece|Urry|Cain|2008|p = 602}} even in the seed plants, where the gametophyte itself is nurtured by its parent sporophyte.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 619–620}} Other groups of organisms that were previously studied by botanists include bacteria (now studied in [[bacteriology]]), fungi ([[mycology]]) – including [[lichen]]-forming fungi ([[lichenology]]), non-[[Chlorophyta|chlorophyte]] [[algae]] ([[phycology]]), and viruses ([[virology]]). However, attention is still given to these groups by botanists, and fungi (including lichens) and photosynthetic [[protist]]s are usually covered in introductory botany courses.{{sfn|Capon|2005|pp = 10–11}}{{sfn|Mauseth|2003|pp = 1–3}}

[[Paleobotany|Palaeobotanists]] study ancient plants in the fossil record to provide information about the [[evolutionary history of plants]]. [[Cyanobacteria]], the first oxygen-releasing photosynthetic organisms on Earth, are thought to have given rise to the ancestor of plants by entering into an [[endosymbiotic]] relationship with an early eukaryote, ultimately becoming the [[chloroplast]]s in plant cells. The new photosynthetic plants (along with their algal relatives) accelerated the rise in atmospheric [[oxygen]] started by the [[cyanobacteria]], [[great oxygenation event|changing]] the ancient oxygen-free, [[Redox|reducing]], atmosphere to one in which free oxygen has been abundant for more than 2 billion years.{{sfn|Cleveland Museum of Natural History|2012}}{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 516–517}}

Among the important botanical questions of the 21st century are the role of plants as primary producers in the global cycling of life's basic ingredients: energy, carbon, oxygen, nitrogen and water, and ways that our plant stewardship can help address the global environmental issues of [[resource management]], [[Conservation (ethic)|conservation]], [[food security|human food security]], [[introduced species|biologically invasive organisms]], [[carbon sequestration]], [[climate change]], and [[sustainability]].{{sfn|Botanical Society of America|2013}}

=== Human nutrition ===

{{further information|Human nutrition}}

[[File:Brown rice.jpg|right|thumb|Alt=grains of brown rice, a staple food|The food we eat comes directly or indirectly from plants such as rice.]]

Virtually all staple foods come either directly from [[primary production]] by plants, or indirectly from animals that eat them.{{sfn|Ben-Menahem|2009|pp = 5367–5368}} Plants and other photosynthetic organisms are at the base of most [[food chain]]s because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be used by animals. This is what ecologists call the first [[trophic level]].{{sfn|Butz|2007|pp = 534–553}} The modern forms of the major [[staple food]]s, such as maize, rice, wheat and other cereal grasses, [[Pulse (legume)|pulses]], bananas and plantains,{{sfn|Stover|Simmonds|1987|pp = 106–126}} as well as [[flax]] and cotton grown for their fibres, are the outcome of prehistoric selection over thousands of years from among [[Neolithic founder crops|wild ancestral plants]] with the most desirable characteristics.{{sfn|Zohary|Hopf|2000|pp = 20–22}}

Botanists study how plants produce food and how to increase yields, for example through [[plant breeding]], making their work important to mankind's ability to feed the world and provide [[food security]] for future generations.{{sfn|Floros|Newsome|Fisher|2010}} Botanists also study weeds, which are a considerable problem in agriculture, and the biology and control of [[Plant pathology|plant pathogens]] in agriculture and natural [[ecosystems]].{{sfn|Schoening|2005}} [[Ethnobotany]] is the study of the relationships between plants and people. When applied to the investigation of historical plant–people relationships ethnobotany may be referred to as archaeobotany or [[paleoethnobotany|palaeoethnobotany]].{{sfn|Acharya|Anshu|2008|p = 440}} Some of the earliest plant-people relationships arose between the [[Indigenous peoples of the Americas|indigenous people]] of Canada in identifying edible plants from inedible plants.<ref name=":1">{{Cite book|url=https://books.google.com/books?id=fPDErXqH8YYC|title=Traditional Plant Foods of Canadian Indigenous Peoples: Nutrition, Botany, and Use|last=Kuhnlein|first=Harriet V.|last2=Turner|first2=Nancy J.|date=1991-01-01|publisher=Taylor & Francis|isbn=9782881244650|language=en}}</ref> This relationship the indigenous people had with plants was recorded by ethnobotanists.<ref name=":1" />

== Plant biochemistry ==

Plant biochemistry is the study of the chemical processes used by plants. Some of these processes are used in their [[primary metabolism]] like the photosynthetic [[Calvin cycle]] and [[crassulacean acid metabolism]].{{sfn|Lüttge|2006|pp = 7–25}} Others make specialised materials like the [[cellulose]] and [[lignin]] used to build their bodies, and [[Secondary metabolism|secondary products]] like [[resin]]s and [[aroma compounds]].

<div style="position: relative; margin-left: 5px; margin-right: 10px; width: 100px; height: 491px; float: left; <!--border: 1px rgba(0,0,0,0.2) solid;--> box-shadow: 1px 1px 3px rgba(0,0,0,0.2);">

<div style="position: absolute;" >[[File:Chromatography.jpg|Alt=A paper chromatogram of spinach leaf extract showing separation of the various pigments in their chloroplasts|[[Paper chromatography]] of some [[spinach]] leaf extract shows the various pigments present in their chloroplasts.|100px]]</div>

<div style="position: absolute; width: 90px; font-size: 90%; line-height: 120%; margin: 5px;" >Plants make various [[photosynthetic pigments]], some of which can be seen here through [[paper chromatography]].</div>

<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:245px;">[[Xanthophylls|<span style="color:#e2c000;">'''Xanthophylls'''</span>]]</div>

<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:272px;">[[Chlorophyll a|<span style="color:#00bb90;">'''Chlorophyll ''a'''''</span>]]</div>

<div style="position:absolute; width:100px; left:0; font-size:90%; line-height:120%; text-align:center; top:300px;">[[Chlorophyll b|<span style="color:#00bb34;">'''Chlorophyll ''b'''''</span>]]</div>

</div>

Plants and various other groups of photosynthetic eukaryotes collectively known as "[[algae]]" have unique organelles known as [[chloroplast]]s. Chloroplasts are thought to be descended from [[cyanobacteria]] that formed [[endosymbiotic]] relationships with ancient plant and algal ancestors. Chloroplasts and cyanobacteria contain the blue-green pigment [[chlorophyll a|chlorophyll ''a'']].{{sfn|Campbell|Reece|Urry|Cain|2008|pp=190–193}} Chlorophyll ''a'' (as well as its plant and green algal-specific cousin [[chlorophyll b|chlorophyll ''b'']]){{efn|Chlorophyll ''b'' is also found in some cyanobacteria. A bunch of other chlorophylls exist in [[cyanobacteria]] and certain algal groups, but none of them are found in land plants.{{sfn|Kim|Archibald|2009|pp=1–39}}{{sfn|Howe|Barbrook|Nisbet|Lockhart|2008|pp=2675–2685}}{{sfn|Takaichi|2011|pp=1101–1118}}}} absorbs light in the blue-violet and orange/red parts of the [[visible spectrum|spectrum]] while reflecting and transmitting the green light that we see as the characteristic colour of these organisms. The energy in the red and blue light that these pigments absorb is used by chloroplasts to make energy-rich carbon compounds from carbon dioxide and water by [[Carbon fixation#Oxygenic photosynthesis|oxygenic photosynthesis]], a process that generates [[molecular oxygen]] (O₂) as a by-product.

{{Plain image|File:Calvin-cycle4.svg|'''The Calvin cycle''' ''(Interactive diagram)'' The [[Calvin cycle]] incorporates carbon dioxide into sugar molecules.|435px|right|top|triangle|#ccc|image override=}}

{{Calvin cycle|Alt=An interactive diagram of the Calvin cycle|caption='''Calvin cycle''' ''(Interactive diagram)''}}

The light energy captured by [[chlorophyll a|chlorophyll ''a'']] is initially in the form of electrons (and later a [[proton gradient]]) that's used to make molecules of [[Adenosine triphosphate|ATP]] and [[NADPH]] which temporarily store and transport energy. Their energy is used in the [[light-independent reactions]] of the Calvin cycle by the enzyme [[rubisco]] to produce molecules of the 3-carbon sugar [[glyceraldehyde 3-phosphate]] (G3P). Glyceraldehyde 3-phosphate is the first product of photosynthesis and the raw material from which [[glucose]] and almost all other organic molecules of biological origin are synthesised. Some of the glucose is converted to starch which is stored in the chloroplast.{{sfn|Lewis|McCourt|2004|pp=1535–1556}} Starch is the characteristic energy store of most land plants and algae, while [[inulin]], a polymer of [[fructose]] is used for the same purpose in the sunflower family [[Asteraceae]]. Some of the glucose is converted to [[sucrose]] (common table sugar) for export to the rest of the plant.

Unlike in animals (which lack chloroplasts), plants and their eukaryote relatives have delegated many biochemical roles to their [[chloroplast]]s, including synthesising all their [[fatty acids]],{{sfn|Padmanabhan|Dinesh-Kumar|2010|pp=1368–1380}}{{sfn|Schnurr|Shockey|De Boer|Browse|2002|pp=1700–1709}} and most [[amino acids]].{{sfn|Ferro|Salvi|Rivière-Rolland|Vermat|2002|pp=11487–11492}} The fatty acids that chloroplasts make are used for many things, such as providing material to build [[cell membranes]] out of and making the polymer [[cutin]] which is found in the [[plant cuticle]] that protects land plants from drying out. {{sfn|Kolattukudy|1996|pp=83–108}}

Plants synthesise a number of unique [[polymer]]s like the [[polysaccharide]] molecules [[cellulose]], [[pectin]] and [[xyloglucan]]{{sfn|Fry|1989|pp=1–11}} from which the land plant cell wall is constructed.{{sfn|Thompson|Fry|2001|pp=23–34}}

Vascular land plants make [[lignin]], a polymer used to strengthen the [[secondary cell walls]] of xylem [[tracheid]]s and [[Xylem vessel element|vessels]] to keep them from collapsing when a plant sucks water through them under water stress. Lignin is also used in other cell types like [[Ground tissue#Sclerenchyma|sclerenchyma fibres]] that provide structural support for a plant and is a major constituent of wood. [[Sporopollenin]] is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. It is widely regarded as a marker for the start of land plant evolution during the [[Ordovician]] period.{{sfn|Kenrick|Crane|1997|pp=33–39}}

The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the [[Ordovician]] and [[Silurian]] periods. Many [[monocots]] like [[maize]] and the [[pineapple]] and some [[dicots]] like the [[Asteraceae]] have since independently evolved{{sfn|Gowik|Westhoff|2010|pp=56–63}} pathways like [[Crassulacean acid metabolism]] and the [[C4 carbon fixation|{{C4}} carbon fixation]] pathway for photosynthesis which avoid the losses resulting from [[photorespiration]] in the more common [[C3 carbon fixation|{{C3}} carbon fixation]] pathway. These biochemical strategies are unique to land plants.

=== Medicine and materials ===

[[File:Tapping a rubber tree in Thailand.JPG|thumb|left|Alt=Plantation worker tapping a rubber tree|Tapping a rubber tree in Thailand]]

[[Phytochemistry]] is a branch of plant biochemistry primarily concerned with the chemical substances produced by plants during [[secondary metabolism]].{{sfn|Benderoth|Textor|Windsor|Mitchell-Olds|2006|pp = 9118–9123}} Some of these compounds are toxins such as the [[alkaloid]] [[coniine]] from [[conium|hemlock]]. Others, such as the [[essential oil]]s [[Peppermint#Peppermint oil|peppermint oil]] and lemon oil are useful for their aroma, as flavourings and spices (e.g., [[capsaicin]]), and in medicine as pharmaceuticals as in [[opium]] from [[Papaver somniferum|opium poppies]]. Many [[medication|medicinal]] and [[recreational drugs]], such as [[tetrahydrocannabinol]] (active ingredient in [[Cannabis (drug)|cannabis]]), [[caffeine]], [[morphine]] and [[nicotine]] come directly from plants. Others are simple [[Derivative (chemistry)|derivatives]] of botanical natural products. For example, the pain killer [[aspirin]] is the acetyl [[ester]] of [[salicylic acid]], originally isolated from the [[Bark (botany)|bark]] of [[willow]] trees,{{sfn|Jeffreys|2005|pp = 38–40}} and a wide range of [[opiate]] [[analgesics|painkillers]] like [[diamorphine|heroin]] are obtained by chemical modification of [[morphine]] obtained from the [[opium poppy]].{{sfn|Mann|1987|pp = 186–187}} Popular [[stimulant]]s come from plants, such as [[caffeine]] from coffee, tea and chocolate, and [[nicotine]] from tobacco. Most alcoholic beverages come from [[fermentation (food)|fermentation]] of [[carbohydrate]]-rich plant products such as [[barley]] (beer), rice ([[sake]]) and grapes (wine).{{sfn|University of Maryland Medical Center|2011}} [[Native Americans in the United States|Native Americans]] have used various plants as ways of treating illness or disease for thousands of years.<ref>{{Cite book|title=How Indians Use Wild Plants for Food, Medicine, and Crafts|last=Frances|first=Densmore|publisher=Dover Publications|year=1974|isbn=9780486131108|location=|pages=}}</ref> This knowledge Native Americans have on plants has been recorded by [[Ethnobotany|enthnobotanists]] and then in turn has been used by [[Pharmaceutical industry|pharmaceutical companies]] as a way of [[drug discovery]].<ref>{{Cite journal|last=McCutcheon|first=A. R.|last2=Ellis|first2=S. M.|last3=Hancock|first3=R. E.|last4=Towers|first4=G. H.|date=1992-10-01|title=Antibiotic screening of medicinal plants of the British Columbian native peoples|journal=Journal of Ethnopharmacology|volume=37|issue=3|pages=213–223|issn=0378-8741|pmid=1453710|doi=10.1016/0378-8741(92)90036-q}}</ref>

Plants can synthesise useful coloured dyes and pigments such as the [[anthocyanin]]s responsible for the red colour of [[red wine]], yellow [[Reseda luteola|weld]] and blue [[Isatis tinctoria|woad]] used together to produce [[Lincoln green]], [[indoxyl]], source of the blue dye [[indigo]] traditionally used to dye denim and the artist's pigments [[gamboge]] and [[rose madder]].

Sugar, [[starch]], cotton, [[linen]], [[hemp]], some types of [[rope]], wood and [[particle board]]s, [[papyrus]] and paper, [[vegetable oil]]s, [[epicuticular wax|wax]], and [[natural rubber]] are examples of commercially important materials made from plant tissues or their secondary products. [[Charcoal]], a pure form of carbon made by [[pyrolysis]] of wood, has a long [[charcoal#History|history]] as a metal-[[smelting]] fuel, as a filter material and [[activated carbon#Applications|adsorbent]] and as an artist's material and is one of the three ingredients of [[gunpowder]]. [[Cellulose]], the world's most abundant organic polymer,{{sfn|Klemm|Heublein|Fink|Bohn|2005}} can be converted into energy, fuels, materials and chemical feedstock. [[cellulose#products|Products made from cellulose]] include [[rayon]] and [[cellophane]], [[methyl cellulose|wallpaper paste]], [[Butanol fuel#Using Alternate Carbon Sources|biobutanol]] and [[nitrocellulose|gun cotton]]. [[Sugarcane]], [[rapeseed]] and [[soy]] are some of the plants with a highly fermentable sugar or oil content that are used as sources of [[biofuel]]s, important alternatives to [[fossil fuel]]s, such as [[biodiesel]].{{sfn|Scharlemann|Laurance|2008|pp = 52–53}} Sweetgrass was used by NativeAmericanse to ward of bugs like [[mosquito]]es.<ref name=":2">{{Cite web|url=https://www.washingtonpost.com/news/morning-mix/wp/2015/08/18/research-confirms-native-american-use-of-sweetgrass-as-bug-repellent/|title=Research confirms Native American use of sweetgrass as bug repellent|website=Washington Post|access-date=2016-05-05}}</ref> These bug repelling properties of sweetgrass were later found by the [[American Chemical Society]] in the molecules [[phytol]] and [[coumarin]].<ref name=":2" />

== Plant ecology ==

{{plain image|File:Lifezones Pengo, IRI.svg|[[Holdridge life zones]] model relationships between vegetation type, moisture availability and temperature.|375px|right|top|triangle|#aaa}}

{{Main article|Plant ecology}}

Plant ecology is the science of the functional relationships between plants and their [[habitat]]s—the environments where they complete their [[Biological life cycle|life cycles]]. Plant ecologists study the composition of local and regional [[flora]]s, their [[biodiversity]], genetic diversity and [[Fitness (biology)|fitness]], the [[adaptation]] of plants to their environment, and their competitive or [[mutualism (biology)|mutualistic]] interactions with other species.{{sfn|Mauseth|2003|pp = 786–818}} Some ecologists even rely on [[Empirical evidence|empirical data]] from indigenous people that is gathered by ethnobotanists.<ref name="TeachEthnobotany">{{Citation|last=TeachEthnobotany|title=Cultivation of peyote by Native Americans: Past, present and future|date=2012-06-12|url=https://www.youtube.com/watch?v=xK5ZjSiIEGE|accessdate=2016-05-05}}</ref> This information can relay a great deal of information on how the land once was thousands of years ago and how it has changed over that time.<ref name="TeachEthnobotany"/> The goals of plant ecology are to understand the causes of their distribution patterns, productivity, environmental impact, evolution, and responses to environmental change.{{sfn|Burrows|1990|pp = 1–73}}

Plants depend on certain [[edaphic]] (soil) and climatic factors in their environment but can modify these factors too. For example, they can change their environment's [[albedo]], increase [[Surface runoff|runoff]] interception, stabilise mineral soils and develop their organic content, and affect local temperature. Plants compete with other organisms in their [[ecosystem]] for resources.{{sfn|Addelson|2003}}{{sfn|Grime|Hodgson|1987|pp = 283–295}} They interact with their neighbours at a variety of [[spatial scale]]s in groups, populations and [[Community (ecology)|communities]] that collectively constitute vegetation. Regions with characteristic [[Holdridge life zones|vegetation types]] and dominant plants as well as similar [[Abiotic component|abiotic]] and [[Biotic components|biotic]] factors, [[climate]], and [[geography]] make up [[biomes]] like [[tundra]] or [[tropical rainforest]].{{sfn|Mauseth|2003|pp = 819–848}}

[[File:Medicago italica root nodules 2.JPG|thumb|left|Alt=Colour photograph of roots of Medicago italica, showing root nodules|The [[root nodule|nodules]] of ''[[Medicago italica]]'' contain the [[nitrogen fixation|nitrogen fixing]] bacterium ''[[Sinorhizobium meliloti]]''. The plant provides the bacteria with nutrients and an [[hypoxia (environmental)|anaerobic]] environment, and the bacteria [[nitrogen fixation|fix nitrogen]] for the plant.{{sfn|Campbell|Reece|Urry|Cain|2008|p=794}}]]

[[Herbivore]]s eat plants, but plants can [[plant defence against herbivory|defend themselves]] and some species are [[parasitic plant|parasitic]] or even [[carnivorous plant|carnivorous]]. Other organisms form [[mutualism (biology)|mutually]] beneficial relationships with plants. For example, [[mycorrhiza]]l fungi and [[rhizobia]] provide plants with nutrients in exchange for food, [[ant]]s are recruited by [[myrmecophyte|ant plants]] to provide protection,{{sfn|Herrera|Pellmyr|2002|pp = 211–235}} [[honey bee]]s, [[bat]]s and other animals [[pollinate]] flowers{{sfn|Proctor|Yeo|1973|p = 479}}{{sfn|Herrera|Pellmyr|2002|pp = 157–185}} and [[seed dispersal#Dispersal by humans|humans]] and [[seed dispersal#Dispersal by animals|other animals]]{{sfn|Herrera|Pellmyr|2002|pp = 185–210}} act as [[dispersal vector]]s to spread [[spore]]s and [[seed]]s.

=== Plants, climate and environmental change ===

Plant responses to climate and other environmental changes can inform our understanding of how these changes affect ecosystem function and productivity. For example, plant [[phenology]] can be a useful [[proxy (climate)|proxy]] for temperature in [[historical climatology]], and the biological impact of [[climate change]] and [[global warming]]. [[Palynology]], the analysis of fossil pollen deposits in sediments from [[geologic timescale|thousands or millions of years ago]] allows the reconstruction of past climates.{{sfn|Bennett|Willis|2001|pp = 5–32}} Estimates of atmospheric {{CO2}} concentrations since the [[Palaeozoic]] have been obtained from [[stomatal]] densities and the leaf shapes and sizes of ancient [[land plants]].{{sfn|Beerling|Osborne|Chaloner|2001|pp = 287–394}} [[Ozone depletion]] can expose plants to higher levels of [[Ultraviolet|ultraviolet radiation-B]] (UV-B), resulting in lower growth rates.{{sfn|Björn|Callaghan|Gehrke|Johanson|1999|pp = 449–454}} Moreover, information from studies of [[community (ecology)|community ecology]], plant [[systematics]], and [[taxonomy (biology)|taxonomy]] is essential to understanding [[climate change#Vegetation|vegetation change]], [[habitat destruction]] and [[endangered species|species extinction]].{{sfn|Ben-Menahem|2009|pp = 5369–5370}}

== Genetics ==

{{Main article|Plant genetics}}

{{plain image|File:Punnett square mendel flowers.svg|A [[Punnett square]] depicting a cross between two pea plants [[heterozygous]] for purple (B) and white (b) blossoms|250px|left|bottom|triangle|#51e89e}}

Inheritance in plants follows the same fundamental principles of genetics as in other multicellular organisms. [[Gregor Mendel]] discovered the [[Mendelian inheritance|genetic laws of inheritance]] by studying inherited traits such as shape in ''Pisum sativum'' ([[peas]]). What Mendel learned from studying plants has had far reaching benefits outside of botany. Similarly, "[[transposon|jumping genes]]" were discovered by [[Barbara McClintock]] while she was studying maize.{{sfn|Ben-Menahem|2009|p = 5369}} Nevertheless, there are some distinctive genetic differences between plants and other organisms.

Species boundaries in plants may be weaker than in animals, and cross species [[hybrid (biology)|hybrids]] are often possible. A familiar example is [[peppermint]], ''Mentha'' × ''piperita'', a [[Sterility (physiology)|sterile]] hybrid between ''[[Mentha aquatica]]'' and spearmint, ''[[Mentha spicata]]''.{{sfn|Stace|2010b||pp = 629–633}} The many cultivated varieties of wheat are the result of multiple inter- and intra-[[species|specific]] crosses between wild species and their hybrids.{{sfn|Hancock|2004|pp = 190–196}} [[Angiosperms]] with [[monoecious]] flowers often have [[Self-incompatibility in plants|self-incompatibility mechanisms]] that operate between the [[pollen]] and [[stigma (botany)|stigma]] so that the pollen either fails to reach the stigma or fails to [[germinate]] and produce male [[gamete]]s.{{sfn|Sobotka|Sáková|Curn|2000|pp = 103–112}} This is one of several methods used by plants to promote [[plant reproductive morphology|outcrossing]].{{sfn|Renner|Ricklefs|1995|pp = 596–606}} In many land plants the male and female gametes are produced by separate individuals. These species are said to be [[Plant reproductive morphology#Terminology|dioecious]] when referring to vascular plant [[sporophyte]]s and [[monoecious|dioicous]] when referring to [[bryophyte]] [[gametophyte]]s.{{sfn|Porley|Hodgetts|2005|pp = 2–3}}

Unlike in higher animals, where [[parthenogenesis]] is rare, [[asexual reproduction]] may occur in plants by several different mechanisms. The formation of stem [[tuber]]s in potato is one example. Particularly in [[arctic]] or [[alpine climate|alpine]] habitats, where opportunities for fertilisation of flowers [[zoophily|by animals]] are rare, plantlets or [[bulbs]], may develop instead of flowers, replacing [[sexual reproduction]] with [[asexual reproduction]] and giving rise to [[cloning|clonal populations]] genetically identical to the parent. This is one of several types of [[apomixis]] that occur in plants. Apomixis can also happen in a [[seed]], producing a seed that contains an embryo genetically identical to the parent.{{sfn|Savidan|2000|pp = 13–86}}

Most [[sexually reproducing]] organisms are diploid, with paired chromosomes, but doubling of their [[chromosome number]] may occur due to errors in [[cell division|cytokinesis]]. This can occur early in development to produce an [[autopolyploid]] or partly autopolyploid organism, or during normal processes of cellular differentiation to produce some cell types that are polyploid ([[endopolyploidy]]), or during [[gamete]] formation. An [[allopolyploid]] plant may result from a [[hybridization event|hybridisation event]] between two different species. Both autopolyploid and allopolyploid plants can often reproduce normally, but may be unable to cross-breed successfully with the parent population because there is a mismatch in chromosome numbers. These plants that are [[reproductively isolated]] from the parent species but live within the same geographical area, may be sufficiently successful to form a new [[sympatric speciation|species]].{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 495–496}} Some otherwise sterile plant polyploids can still reproduce [[vegetative propagation|vegetatively]] or by seed apomixis, forming clonal populations of identical individuals.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 495–496}} [[Durum]] wheat is a fertile [[tetraploid]] allopolyploid, while [[common wheat|bread wheat]] is a fertile [[hexaploid]]. The commercial banana is an example of a sterile, seedless [[triploid]] hybrid. [[Taraxacum officinale|Common dandelion]] is a triploid that produces viable seeds by apomictic seed.

As in other eukaryotes, the inheritance of [[endosymbiotic]] organelles like [[mitochondria]] and [[chloroplast]]s in plants is non-[[Mendelian]]. Chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants.{{sfn|Morgensen|1996|pp = 383–384}}

=== Molecular genetics ===

{{further information|Molecular genetics}}

[[File:Arabidopsis thaliana inflorescencias.jpg|thumb|Alt=Flowers of Arabidopsis thaliana, the most important model plant and the first to have its genome sequenced|Thale cress, ''[[Arabidopsis thaliana]]'', the first plant to have its genome sequenced, remains the most important model organism.]]

A considerable amount of new knowledge about plant function comes from studies of the molecular genetics of [[model organism#Plants|model plants]] such as the Thale cress, ''[[Arabidopsis thaliana]]'', a weedy species in the mustard family ([[Brassicaceae]]).{{sfn|Benderoth|Textor|Windsor|Mitchell-Olds|2006|pp = 9118–9123}} The [[genome]] or hereditary information contained in the genes of this species is encoded by about 135 million [[base pairs]] of DNA, forming one of the smallest genomes among [[flowering plants]]. ''Arabidopsis'' was the first plant to have its genome sequenced, in 2000.{{sfn|Arabidopsis Genome Initiative|2000|pp = 796–815}} The sequencing of some other relatively small genomes, of rice (''[[Oryza sativa]]''){{sfn|Devos|Gale|2000}} and ''[[Brachypodium distachyon]]'',{{sfn|University of California-Davis|2012}} has made them important model species for understanding the genetics, cellular and molecular biology of [[cereals]], [[grasses]] and [[monocots]] generally.

[[Model organism#Plants|Model plants]] such as ''[[Arabidopsis thaliana]]'' are used for studying the molecular biology of [[plant cell]]s and the [[chloroplast]]. Ideally, these organisms have small genomes that are well known or completely sequenced, small stature and short generation times. Corn has been used to study mechanisms of [[photosynthesis]] and [[phloem]] loading of sugar in [[C4 plants|{{C4}} plants]].{{sfn|Russin|Evert|Vanderveer|Sharkey|1996|pp = 645–658}} The [[single celled]] [[green alga]] ''[[Chlamydomonas reinhardtii]]'', while not an [[embryophyte]] itself, contains a [[chlorophyll b|green-pigmented]] [[Chloroplast#Chloroplastida (green algae and plants)|chloroplast]] related to that of land plants, making it useful for study.{{sfn|Rochaix|Goldschmidt-Clermont|Merchant|1998|p = 550}} A [[red alga]] ''[[Cyanidioschyzon merolae]]'' has also been used to study some basic chloroplast functions.{{sfn|Glynn|Miyagishima|Yoder|Osteryoung|2007|pages = 451–461}} [[Spinach]],{{sfn|Possingham|Rose|1976|pp = 295–305}} [[peas]],{{sfn|Sun|Forouhar|Li|Tu|2002|pp = 95–100}} [[soybeans]] and a moss ''[[Physcomitrella patens]]'' are commonly used to study plant cell biology.{{sfn|Heinhorst|Cannon|1993|pp = 1–9}}

''[[Agrobacterium tumefaciens]]'', a soil [[rhizosphere]] bacterium, can attach to plant cells and infect them with a [[Callus (cell biology)|callus]]-inducing [[Ti plasmid]] by [[horizontal gene transfer]], causing a callus infection called crown gall disease. Schell and Van Montagu (1977) hypothesised that the Ti plasmid could be a natural vector for introducing the [[Nif gene]] responsible for [[nitrogen fixation]] in the root nodules of [[Fabaceae|legumes]] and other plant species.{{sfn|Schell|Van Montagu|1977|pp = 159–179}} Today, genetic modification of the Ti plasmid is one of the main techniques for introduction of [[transgene]]s to plants and the creation of [[genetically modified crops]].

=== Epigenetics ===

{{Main article|Epigenetics}}

[[Epigenetics]] is the study of heritable changes in [[gene expression|gene function]] that cannot be explained by changes in the underlying [[DNA sequence]]{{sfn|Bird|2007|pp = 396–398}} but cause the organism's genes to behave (or "express themselves") differently.{{sfn|Hunter|2008}} One example of epigenetic change is the marking of the genes by [[DNA methylation]] which determines whether they will be expressed or not. Gene expression can also be controlled by repressor proteins that attach to [[silencer (DNA)|silencer]] regions of the DNA and prevent that region of the DNA code from being expressed. Epigenetic marks may be added or removed from the DNA during programmed stages of development of the plant, and are responsible, for example, for the differences between anthers, petals and normal leaves, despite the fact that they all have the same underlying genetic code. Epigenetic changes may be temporary or may remain through successive [[cell division]]s for the remainder of the cell's life. Some epigenetic changes have been shown to be [[Heritability|heritable]],{{sfn|Spector|2012|p = 8}} while others are reset in the germ cells.

Epigenetic changes in [[Eukaryote|eukaryotic]] biology serve to regulate the process of [[cellular differentiation]]. During [[morphogenesis]], [[totipotent]] [[stem cells]] become the various [[pluripotent]] [[cell line]]s of the [[embryo]], which in turn become fully differentiated cells. A single fertilised egg cell, the [[zygote]], gives rise to the many different [[plant cell]] types including [[parenchyma]], [[vessel element|xylem vessel elements]], [[phloem]] sieve tubes, [[guard cell]]s of the [[epidermis (botany)|epidermis]], etc. as it continues to [[mitosis|divide]]. The process results from the epigenetic activation of some genes and inhibition of others.{{sfn|Reik|2007|pp = 425–432}}

Unlike animals, many plant cells, particularly those of the [[ground tissue#Parenchyma|parenchyma]], do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. Exceptions include highly lignified cells, the [[ground tissue#Sclerenchyma|sclerenchyma]] and xylem which are dead at maturity, and the phloem sieve tubes which lack nuclei. While plants use many of the same epigenetic mechanisms as animals, such as [[chromatin remodeling|chromatin remodelling]], an alternative hypothesis is that plants set their gene expression patterns using positional information from the environment and surrounding cells to determine their developmental fate.{{sfn|Costa|Shaw|2007|pp = 101–106}}

== Plant evolution ==

{{Main article|Evolutionary history of plants}}

[[File:Rhynia stem.jpg|thumb|left|Alt=colour image of a cross section of a fossil stem of ''Rhynia gwynne-vaughanii'', a Devonian vascular plant|Transverse section of a fossil stem of the Devonian vascular plant ''[[Rhynia]] gwynne-vaughani'']]

The [[chloroplast]]s of plants have a number of biochemical, structural and genetic similarities to [[cyanobacteria]], (commonly but incorrectly known as "blue-green algae") and are thought to be derived from an ancient [[endosymbiotic theory|endosymbiotic]] relationship between an ancestral [[eukaryote|eukaryotic cell]] and a [[Chloroplast#Cyanobacterial ancestor|cyanobacterial resident]].{{sfn|Mauseth|2003|pp = 552–581}}{{sfn|Copeland|1938|pp = 383–420}}{{sfn|Woese et al.|1977|pp = 305–311}}{{sfn|Cavalier-Smith|2004|pp = 1251–1262}}

The [[algae]] are a [[Polyphyly|polyphyletic]] group and are placed in various divisions, some more closely related to plants than others. There are many differences between them in features such as cell wall composition, biochemistry, pigmentation, chloroplast structure and nutrient reserves. The algal division [[Charophyta]], sister to the green algal division [[Chlorophyta]], is considered to contain the ancestor of true plants.{{sfn|Mauseth|2003|pp = 617–654}} The Charophyte class [[Charophyceae]] and the land plant sub-kingdom [[Embryophyta]] together form the [[monophyletic]] group or clade [[Streptophytina]].{{sfn|Becker|Marin|2009|pp = 999–1004}}

Nonvascular land plants are [[embryophyte]]s that lack the vascular tissues [[xylem]] and [[phloem]]. They include [[moss]]es, [[Marchantiophyta|liverworts]] and [[hornwort]]s. [[Pteridophyte|Pteridophytic]] vascular plants with true xylem and phloem that reproduced by spores germinating into free-living gametophytes evolved during the Silurian period and diversified into several lineages during the late [[Silurian]] and early [[Devonian]]. Representatives of the lycopods have survived to the present day. By the end of the Devonian period, several groups, including the [[Lycopodiophyta|lycopods]], [[Sphenophyllales|sphenophylls]] and [[progymnosperm]]s, had independently evolved "megaspory" – their spores were of two distinct sizes, larger [[megaspore]]s and smaller microspores. Their reduced gametophytes developed from megaspores retained within the [[sporangium|spore-producing organs]] (megasporangia) of the sporophyte, a condition known as endospory. Seeds consist of an endosporic megasporangium surrounded by one or two sheathing layers ([[integument]]s). The young sporophyte develops within the seed, which on [[germination]] splits to release it. The earliest known seed plants date from the latest Devonian [[Famennian]] stage.{{sfn|Fairon-Demaret|1996|pp = 217–233}}{{sfn|Stewart|Rothwell|1993|pp = 279–294}} Following the evolution of the seed habit, [[Spermatophyte|seed plants]] diversified, giving rise to a number of now-extinct groups, including [[Pteridospermatophyta|seed ferns]], as well as the modern [[gymnosperm]]s and [[angiosperms]].{{sfn|Taylor|Taylor|Krings|2009|loc = chapter 13}} [[Gymnosperm]]s produce "naked seeds" not fully enclosed in an ovary; modern representatives include [[Pinophyta|conifers]], [[cycad]]s, ''[[Ginkgo]]'', and [[Gnetophyta|Gnetales]]. Angiosperms produce seeds enclosed in a structure such as a [[Gynoecium|carpel]] or an [[ovary]].{{sfn|Mauseth|2003|pp = 720–750}}{{sfn|Mauseth|2003|pp = 751–785}} Ongoing research on the molecular phylogenetics of living plants appears to show that the angiosperms are a [[sister clade]] to the gymnosperms.{{sfn|Lee|Cibrian-Jaramillo|Kolokotronis|Katari|2011|p = e1002411}}

== Plant physiology ==

{{further information|Plant physiology}}

[[File:Plant physiology.png|thumb|right|275px|Alt=A Venn diagram of the relationships between five key areas of plant physiology|Five of the key areas of study within plant physiology]]

Plant physiology encompasses all the internal chemical and physical activities of plants associated with life.{{sfn|Mauseth|2003|pp = 278–279}} Chemicals obtained from the air, soil and water form the basis of all [[metabolism|plant metabolism]]. The energy of sunlight, captured by oxygenic photosynthesis and released by [[cellular respiration]], is the basis of almost all life. [[Phototroph|Photoautotrophs]], including all green plants, algae and [[cyanobacteria]] gather energy directly from sunlight by photosynthesis. [[Heterotroph]]s including all animals, all fungi, all completely parasitic plants, and non-photosynthetic bacteria take in organic molecules produced by photoautotrophs and respire them or use them in the construction of cells and tissues.{{sfn|Mauseth|2003|pp = 280–314}} [[Cellular respiration|Respiration]] is the oxidation of carbon compounds by breaking them down into simpler structures to release the energy they contain, essentially the opposite of photosynthesis.{{sfn|Mauseth|2003|pp = 315–340}}

Molecules are moved within plants by transport processes that operate at a variety of [[spatial scale]]s. Subcellular transport of ions, electrons and molecules such as water and [[enzyme]]s occurs across [[cell membranes]]. Minerals and water are transported from roots to other parts of the plant in the [[transpiration stream]]. [[Diffusion]], [[osmosis]], and [[active transport]] and [[mass flow]] are all different ways transport can occur.{{sfn|Mauseth|2003|pp = 341–372}} Examples of [[plant nutrition|elements that plants need]] to transport are [[nitrogen]], [[phosphorus]], [[potassium]], [[calcium]], [[magnesium]], and [[sulphur]]. In vascular plants, these elements are extracted from the soil as soluble ions by the roots and transported throughout the plant in the xylem. Most of the elements required for [[plant nutrition]] come from the chemical breakdown of soil minerals.{{sfn|Mauseth|2003|pp = 373–398}} [[Sucrose]] produced by photosynthesis is transported from the leaves to other parts of the plant in the phloem and [[Plant physiology#Plant hormones|plant hormones]] are transported by a variety of processes.

=== Plant hormones ===

[[File:Phototropism Diagram.svg|thumb|275px|Alt=A diagram of the mechanism of phototropism in oat coleoptiles| '''1''' An oat [[coleoptile]] with the sun overhead. [[Auxin]] (pink) is evenly distributed in its tip. <br />'''2''' With the sun at an angle and only shining on one side of the shoot, auxin moves to the opposite side and stimulates [[cell elongation]] there. <br />'''3''' and '''4''' Extra growth on that side causes the shoot to [[phototropism|bend towards the sun]].{{sfn|Mauseth|2012|p=351}}]]

{{further information|Plant hormone|Phytochrome}}

Plants are not passive, but respond to [[signal transduction|external signals]] such as light, touch, and injury by moving or growing towards or away from the stimulus, as appropriate. Tangible evidence of touch sensitivity is the almost instantaneous collapse of leaflets of ''[[Mimosa pudica]]'', the insect traps of [[Venus flytrap]] and [[bladderwort]]s, and the pollinia of orchids.{{sfn|Darwin|1880|pp = 129–200}}

The hypothesis that plant growth and development is coordinated by [[plant hormone]]s or plant growth regulators first emerged in the late 19th century. Darwin experimented on the movements of plant shoots and roots towards [[heliotropism|light]]{{sfn|Darwin|1880|pp = 449–492}} and [[geotropism|gravity]], and concluded "It is hardly an exaggeration to say that the tip of the radicle . . acts like the brain of one of the lower animals . . directing the several movements".{{sfn|Darwin|1880|p = 573}} About the same time, the role of [[auxin]]s (from the Greek auxein, to grow) in control of plant growth was first outlined by the Dutch scientist [[Frits Went]].{{sfn|Plant Hormones|2013}} The first known auxin, [[indole-3-acetic acid]] (IAA), which promotes cell growth, was only isolated from plants about 50 years later.{{sfn|Went|Thimann|1937|pp = 110–112}} This compound mediates the tropic responses of shoots and roots towards light and gravity.{{sfn|Mauseth|2003|pp = 411–412}} The finding in 1939 that plant [[callus (cell biology)|callus]] could be maintained in culture containing IAA, followed by the observation in 1947 that it could be induced to form roots and shoots by controlling the concentration of growth hormones were key steps in the development of plant biotechnology and genetic modification.{{sfn|Sussex|2008|pp = 1189–1198}}

[[File:Venus Fly Trap Eating Compilation Scott's Revenge On The Caterpillars.ogv|thumb|275px|trapping|Alt=a video compilation of Venus's fly trap catching insects|Venus's fly trap, ''Dionaea muscipula'', showing the touch-sensitive insect trap in action]] [[Cytokinin]]s are a class of plant hormones named for their control of cell division or [[cytokinesis]]. The natural cytokinin [[zeatin]] was discovered in corn, ''[[Zea mays]]'', and is a derivative of the [[purine]] [[adenine]]. Zeatin is produced in roots and transported to shoots in the xylem where it promotes cell division, bud development, and the greening of chloroplasts.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 827–830}}{{sfn|Mauseth|2003|pp = 411–413}} The [[gibberelins]], such as [[Gibberelic acid]] are [[diterpene]]s synthesised from [[Acetyl-CoA carboxylase|acetyl CoA]] via the [[mevalonate pathway]]. They are involved in the promotion of germination and dormancy-breaking in seeds, in regulation of plant height by controlling stem elongation and the control of flowering.{{sfn|Taiz|Zeiger|2002|pp = 461–492}} [[Abscisic acid]] (ABA) occurs in all land plants except liverworts, and is synthesised from [[carotenoid]]s in the chloroplasts and other plastids. It inhibits cell division, promotes seed maturation, and dormancy, and promotes stomatal closure. It was so named because it was originally thought to control [[abscission]].{{sfn|Taiz|Zeiger|2002|pp = 519–538}} [[Ethylene#Ethylene as a plant hormone|Ethylene]] is a gaseous hormone that is produced in all higher plant tissues from [[methionine]]. It is now known to be the hormone that stimulates or regulates fruit ripening and abscission,{{sfn|Lin|Zhong|Grierson|2009|pp = 331–336}}{{sfn|Taiz|Zeiger|2002|pp = 539–558}} and it, or the synthetic growth regulator [[ethephon]] which is rapidly metabolised to produce ethylene, are used on industrial scale to promote ripening of cotton, [[pineapple]]s and other [[climacteric (botany)|climacteric]] crops.

Another class of [[phytohormone]]s is the [[jasmonate]]s, first isolated from the oil of ''[[Jasminum grandiflorum]]''{{sfn|Demole|Lederer|Mercier|1962||pp = 675–685}} which regulates wound responses in plants by unblocking the expression of genes required in the [[systemic acquired resistance]] response to pathogen attack.{{sfn|Chini|Fonseca|Fernandez|Adie|2007|pp = 666–671}}

In addition to being the primary energy source for plants, light functions as a signalling device, providing information to the plant, such as how much sunlight the plant receives each day. This can result in adaptive changes in a process known as [[photomorphogenesis]]. [[Phytochrome]]s are the [[Photoreceptor protein|photoreceptors]] in a plant that are sensitive to light.{{sfn|Roux|1984|pp = 25–29}}

== Plant anatomy and morphology ==

[[File:Oryza sativa - Köhler–s Medizinal-Pflanzen-232.jpg|thumb|Alt=Colour image of a 19th-century illustration of the morphology of a rice plant|A nineteenth-century illustration showing the morphology of the roots, stems, leaves and flowers of the rice plant ''[[Oryza sativa]]'']]

[[Plant anatomy]] is the study of the structure of plant cells and tissues, whereas [[plant morphology]] is the study of their external form.{{sfn|Raven|Evert|Eichhorn|2005|p = 9}}

All plants are multicellular eukaryotes, their DNA stored in nuclei.{{sfn|Mauseth|2003|pp = 433–467}}{{sfn|National Center for Biotechnology Information|2004}} The characteristic features of [[plant cell]]s that distinguish them from those of animals and fungi include a primary [[cell wall]] composed of the polysaccharides [[cellulose]], [[hemicellulose]] and [[pectin]], {{sfn|Mauseth|2003|pp = 62–81}} larger [[vacuole]]s than in animal cells and the presence of [[plastid]]s with unique photosynthetic and biosynthetic functions as in the chloroplasts. Other plastids contain storage products such as starch ([[amyloplasts]]) or lipids ([[elaioplast]]s). Uniquely, [[streptophyte]] cells and those of the green algal order [[Trentepohliales]]{{sfn|López-Bautista|Waters|Chapman|2003|pp = 1715–1718}} divide by construction of a [[phragmoplast]] as a template for building a [[cell plate]] late in [[cytokinesis|cell division]].{{sfn|Lewis|McCourt|2004|pp=1535–1556}}

{{plain image|File:Plant.svg|A diagram of a "typical" [[eudicot]], the most common type of plant (three-fifths of all plant species).{{sfn|Campbell|Reece|Urry|Cain|2008|pp=630, 738}} No plant actually looks exactly like this though.|275px|left|bottom|triangle|#43d050}}

The bodies of [[vascular plant]]s including [[Lycopodiopsida|clubmosses]], [[fern]]s and [[spermatophyte|seed plants]] ([[gymnosperm]]s and [[angiosperms]]) generally have aerial and subterranean subsystems. The [[shoot]]s consist of [[Plant stem|stems]] bearing green photosynthesising [[Leaf|leaves]] and reproductive structures. The underground vascularised [[root]]s bear [[root hairs]] at their tips and generally lack chlorophyll.{{sfn|Campbell|Reece|Urry|Cain|2008|p=739}} Non-vascular plants, the [[Marchantiophyta|liverworts]], [[hornworts]] and [[mosses]] do not produce ground-penetrating vascular roots and most of the plant participates in photosynthesis.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 607–608}} The [[sporophyte]] generation is nonphotosynthetic in liverworts but may be able to contribute part of its energy needs by photosynthesis in mosses and hornworts.{{sfn|Lepp|2012}}

The root system and the shoot system are interdependent – the usually nonphotosynthetic root system depends on the shoot system for food, and the usually photosynthetic shoot system depends on water and minerals from the root system.{{sfn|Campbell|Reece|Urry|Cain|2008|p = 739}} Cells in each system are capable of creating cells of the other and producing [[adventitious]] shoots or roots.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 812–814}} [[Stolons]] and [[tuber]]s are examples of shoots that can grow roots.{{sfn|Campbell|Reece|Urry|Cain|2008|p = 740}} Roots that spread out close to the surface, such as those of willows, can produce shoots and ultimately new plants.{{sfn|Mauseth|2003|pp = 185–208}} In the event that one of the systems is lost, the other can often regrow it. In fact it is possible to grow an entire plant from a single leaf, as is the case with ''[[Saintpaulia]]'',{{sfn|Mithila|Hall|Victor|Saxena|2003|pp = 408–414}} or even a single [[Cell (biology)|cell]] – which can dedifferentiate into a [[Callus (cell biology)|callus]] (a mass of unspecialised cells) that can grow into a new plant.{{sfn|Campbell|Reece|Urry|Cain|2008|pp = 812–814}}

In vascular plants, the xylem and phloem are the conductive tissues that transport resources between shoots and roots. Roots are often adapted to store food such as sugars or [[starch]],{{sfn|Campbell|Reece|Urry|Cain|2008|p = 739}} as in [[sugar beet]]s and carrots.{{sfn|Mauseth|2003|pp = 185–208}}

Stems mainly provide support to the leaves and reproductive structures, but can store water in succulent plants such as [[Cactus|cacti]], food as in potato [[tubers]], or [[vegetative reproduction|reproduce vegetatively]] as in the [[stolons]] of [[strawberry#Cultivation|strawberry]] plants or in the process of [[layering]].{{sfn|Campbell|Reece|Urry|Cain|2008|p = 741}} Leaves gather sunlight and carry out [[photosynthesis]].{{sfn|Mauseth|2003|pp = 114–153}} Large, flat, flexible, green leaves are called foliage leaves.{{sfn|Mauseth|2003|pp = 154–184}} [[Gymnosperm]]s, such as [[conifer]]s, [[cycad]]s, ''[[Ginkgo]]'', and [[gnetophyta|gnetophytes]] are seed-producing plants with open seeds.{{sfn|Capon|2005|p = 11}} [[Angiosperms]] are [[Spermatophyte|seed-producing plants]] that produce flowers and have enclosed seeds.{{sfn|Mauseth|2003|pp = 720–750}} Woody plants, such as [[azalea]]s and [[oak]]s, undergo a secondary growth phase resulting in two additional types of tissues: wood (secondary [[xylem]]) and bark (secondary [[phloem]] and [[Cork cambium|cork]]). All gymnosperms and many angiosperms are woody plants.{{sfn|Mauseth|2003|pp = 209–243}} Some plants reproduce sexually, some asexually, and some via both means.{{sfn|Mauseth|2003|pp = 244–277}}

Although reference to major morphological categories such as root, stem, leaf, and trichome are useful, one has to keep in mind that these categories are linked through intermediate forms so that a continuum between the categories results.{{sfn|Sattler|Jeune|1992|pp = 249-269}} Furthermore, structures can be seen as processes, that is, process combinations.{{sfn|Sattler|1992|pp = 708-714}}

== Systematic botany ==

{{further information|Taxonomy (biology)}}

[[File:HerbPrepLG.jpg|thumb|275px|left|Alt=photograph of a botanist preparing plant specimens for the herbarium|A botanist preparing a plant specimen for mounting in the [[herbarium]]]]

Systematic botany is part of systematic biology, which is concerned with the range and diversity of organisms and their relationships, particularly as determined by their evolutionary history.{{sfn|Lilburn|Harrison|Cole|Garrity|2006}} It involves, or is related to, biological classification, scientific taxonomy and [[phylogenetics]]. Biological classification is the method by which botanists group organisms into categories such as [[genus|genera]] or [[species]]. Biological classification is a form of [[Taxonomy (biology)|scientific taxonomy]]. Modern taxonomy is rooted in the work of [[Carl Linnaeus]], who grouped species according to shared physical characteristics. These groupings have since been revised to align better with the [[Charles Darwin|Darwinian]] principle of [[common descent]] – grouping organisms by ancestry rather than [[phenotype|superficial characteristics]]. While scientists do not always agree on how to classify organisms, [[molecular phylogenetics]], which uses [[DNA sequences]] as data, has driven many recent revisions along evolutionary lines and is likely to continue to do so. The dominant classification system is called [[Linnaean taxonomy]]. It includes ranks and [[binomial nomenclature]]. The nomenclature of botanical organisms is codified in the [[International Code of Nomenclature for algae, fungi, and plants]] (ICN) and administered by the [[International Botanical Congress]].{{sfn|McNeill|Barrie|Buck|Demoulin|2011|p = Preamble, para. 7}}{{sfn|Mauseth|2003|pp = 528–551}}

[[Kingdom (biology)|Kingdom]] [[Plant]]ae belongs to [[Domain (biology)|Domain]] [[Eukarya]] and is broken down recursively until each species is separately classified. The order is: [[Kingdom (biology)|Kingdom]]; [[Phylum]] (or Division); [[Class (biology)|Class]]; [[Order (biology)|Order]]; [[Family (biology)|Family]]; [[Genus]] (plural ''genera''); [[Species]]. The scientific name of a plant represents its genus and its species within the genus, resulting in a single worldwide name for each organism.{{sfn|Mauseth|2003|pp = 528–551}} For example, the tiger lily is ''[[Lilium columbianum]]''. ''Lilium'' is the genus, and ''columbianum'' the [[Botanical name#Binary name|specific epithet]]. The combination is the name of the species. When writing the scientific name of an organism, it is proper to capitalise the first letter in the genus and put all of the specific epithet in lowercase. Additionally, the entire term is ordinarily italicised (or underlined when italics are not available).{{sfn|Mauseth|2003|pp = 528–55}}{{sfn|International Association for Plant Taxonomy|2006}}{{sfn|Silyn-Roberts|2000|p = 198}}

The evolutionary relationships and heredity of a group of organisms is called its [[Phylogenetics|phylogeny]]. Phylogenetic studies attempt to discover phylogenies. The basic approach is to use similarities based on shared inheritance to determine relationships.{{sfn|Mauseth|2012|pp = 438–444}} As an example, species of ''[[Pereskia]]'' are trees or bushes with prominent leaves. They do not obviously resemble a typical leafless [[cactus]] such as an ''[[Echinocactus]]''. However, both ''Pereskia'' and ''Echinocactus'' have spines produced from [[areoles]] (highly specialised pad-like structures) suggesting that the two genera are indeed related.{{sfn|Mauseth|2012|pp = 446–449}}{{sfn|Anderson|2001|pp = 26–27}}

{{Multiple image|float=right

|title=Two cacti of very different appearance

|total_width=400

|width1=3872|height1=2592|image1=Pereskia aculeata5.jpg|caption1=''Pereskia aculeata''

|width2=4288|height2=3216|image2=Bogarub-echinocactus-grusonii-1.jpg|caption2=''Echinocactus grusonii''

|footer=Although ''Pereskia'' is a tree with leaves, it has spines and areoles like a more typical cactus, such as ''Echinocactus''.}}

Judging relationships based on shared characters requires care, since plants may resemble one another through [[convergent evolution]] in which characters have arisen independently. Some [[euphorbia]]s have leafless, rounded bodies adapted to water conservation similar to those of globular cacti, but characters such as the structure of their flowers make it clear that the two groups are not closely related. The [[Cladistics|cladistic method]] takes a systematic approach to characters, distinguishing between those that carry no information about shared evolutionary history – such as those evolved separately in different groups ([[homoplasies]]) or those left over from ancestors ([[plesiomorphies]]) – and derived characters, which have been passed down from innovations in a shared ancestor ([[apomorphies]]). Only derived characters, such as the spine-producing areoles of cacti, provide evidence for descent from a common ancestor. The results of cladistic analyses are expressed as [[cladogram]]s: tree-like diagrams showing the pattern of evolutionary branching and descent.{{sfn|Mauseth|2012|pp = 442–450}}

From the 1990s onwards, the predominant approach to constructing phylogenies for living plants has been [[molecular phylogenetics]], which uses molecular characters, particularly [[DNA]] sequences, rather than morphological characters like the presence or absence of spines and areoles. The difference is that the genetic code itself is used to decide evolutionary relationships, instead of being used indirectly via the characters it gives rise to. [[Clive A. Stace|Clive Stace]] describes this as having "direct access to the genetic basis of evolution."{{sfn|Stace|2010a|p = 104}} As a simple example, prior to the use of genetic evidence, fungi were thought either to be plants or to be more closely related to plants than animals. Genetic evidence suggests that the true evolutionary relationship of multicelled organisms is as shown in the cladogram below – fungi are more closely related to animals than to plants.{{sfn|Mauseth|2012|p = 453}}

<div style="float: left; margin-right: 15px; ">{{clade

|1={{clade

|1='''plants'''

|2={{clade

|1='''fungi'''

|2='''animals'''

}}

}}

}}

</div>

In 1998 the [[Angiosperm Phylogeny Group]] published a [[phylogenetics|phylogeny]] for flowering plants based on an analysis of DNA sequences from most families of flowering plants. As a result of this work, many questions, such as which families represent the earliest branches of [[angiosperms]], have now been answered.{{sfn|Burger|2013}} Investigating how plant species are related to each other allows botanists to better understand the process of evolution in plants.{{sfn|Chase et al.|2003|pp = 399–436}} Despite the study of model plants and increasing use of DNA evidence, there is ongoing work and discussion among taxonomists about how best to classify plants into various [[Taxon|taxa]].{{sfn|Capon|2005|p = 223}} Technological developments such as computers and [[electron microscope]]s have greatly increased the level of detail studied and speed at which data can be analysed.{{sfn|Morton|1981|pp = 459–459}}

{{div col|colwidth=17em}}

* [[Agricultural science]]

* [[Bibliography of biology]]

* [[Branches of botany]]

* [[Dendrochronology]]

* [[Evolution of plants]]

* [[Genomics of domestication]]

* [[Glossary of botanical terms]]

* [[Glossary of plant morphology]]

* [[Herbchronology]]

* [[History of phycology]]

* [[History of plant systematics]]

* [[List of botany journals]]

* [[List of botanists]]

* [[List of botanical gardens]]

* [[List of botanists by author abbreviation]]

* [[List of domesticated plants]]

* [[List of flowers]]

* [[List of Russian botanists]]

* [[List of systems of plant taxonomy]]

* [[Outline of botany]]

* [[Plant reproductive morphology]]

* [[Soil science]]

* [[Weed]] science

{{div col end}}

== Footnotes ==

{{notelist}}

== References ==

{{reflist|16em}}

== Bibliography ==

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{{refend}}

== External links ==

{{Wikibooks|Botany}}

{{Commons category|Botany}}

{{WVD}}

{{Wikisource portal|Botany}}

{{Wikivoyage|Botanical tourism}}

* {{dmoz|Science/Biology/Botany/|Botany}}

* [http://huntbot.andrew.cmu.edu/HIBD/Departments/Databases.shtml Botany databases] at the Hunt Institute for Botanical Documentation

* [http://www.kuleuven-kortrijk.be/bioweb/?page=guide&lang=en/ High quality pictures of plants and information about them] from Catholic University of Leuven

* [http://wildflower.utexas.edu/ Native Plant Information Network]

* [http://plants.usda.gov/index.html USDA plant database]

* [http://www.ou.edu/cas/botany-micro/www-vl/ The Virtual Library of Botany]

* [http://ccdl.libraries.claremont.edu/cdm/landingpage/collection/loc Larry Oglesby Collection] in the Claremont Colleges Digital Library