Molecular genetics[edit]

Further information: Molecular geneticsaazzqqwwaa

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 plants such as the Thale cress,Arabidopsis thaliana, a weedy species in the mustard [84] family (Brassicaceae). 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 [113] plants. Arabidopsis was the first plant to have its genome sequenced, in 2000. The sequencing of [114] [115] some other relatively small genomes, of rice (Oryza sativa) and Brachypodium distachyon, has made them important model species for understanding the genetics, cellular and molecular biology of cereals, grasses and monocots generally. Model plants such as Arabidopsis thaliana are used for studying the molecular biology of plant cells 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 [116] of photosynthesisand phloem loading of sugar in C4 plants. The single celled green alga Chlamydomonas reinhardtii, while not an embryophyteitself, contains a green[117] pigmented chloroplast related to that of land plants, making it useful for study. A red algaCyanidioschyzon merolae has also been used to study some basic chloroplast [118] [119] [120] functions. Spinach, peas, soybeansand a moss Physcomitrella patens are commonly used to [121] study plant cell biology. Agrobacterium tumefaciens, a soil rhizosphere bacterium, can attach to plant cells and infect them with a 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 legumes and other plant [122] species. Today, genetic modification of the Ti plasmid is one of the main techniques for introduction of transgenes to plants and the creation of genetically modified crops.

Epigenetics[edit]
Main article: Epigenetics

Epigenetics is the study of mitotically and/or meiotically heritable changes in gene function that cannot be [123] explained by changes in the underlying DNA sequence but cause the organism's genes to behave (or [124] "express themselves") differently. 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 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 divisions for [125] the remainder of the cell's life. Some epigenetic changes have been shown to beheritable, while others are reset in the germ cells. Epigenetic changes in eukaryotic biology serve to regulate the process of cellular differentiation. During morphogenesis, totipotentstem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. A single fertilized egg cell, the zygote, gives rise to the many different plant cell types including parenchyma, xylem vessel elements,phloem sieve tubes, guard cells of the epidermis, etc. as it continues to divide. The process results from the epigenetic activation of some [126] genes and inhibition of others. Unlike animals, many plant cells, particularly those of the parenchyma, do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. Exceptions include highly lignified cells, the 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, an alternative hypothesis is that plants set their gene expression patterns using positional [127] information from the environment and surrounding cells to determine their developmental fate.

Evolution[edit]

Transverse section of a fossil stem of the Devonian vascular plant Rhynia gwynne-vaughani

Main article: Evolutionary history of plants The chloroplasts 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 relationship between an ancestral eukaryotic cell and a cyanobacterial [128][129][130][131] resident. The algae are a 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, [132] sister to the green algal division Chlorophyta, is considered to contain the ancestor of true plants. The Charophyte class Charophyceae and the land plant sub-kingdomEmbryophyta together form [133] the monophyletic group or clade Streptophytina. Nonvascular land plants are embryophytes that lack the vascular tissues xylemand phloem. They include mosses, liverworts and hornworts. Pteridophyticvascular 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 lycopods, sphenophylls and progymnosperms, had independently evolved "megaspory" their spores were of two distinct sizes, larger megaspores and smaller microspores. Their reduced gametophytes developed from megaspores retained within the 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 (integuments). The young sporophyte develops within the seed, which on germination splits to release it. The earliest known seed plants date from the latest [134][135] Devonian Famennian stage. Following the evolution of the seed habit,seed plants diversified, giving rise to a number of now-extinct groups, including seed ferns, as well as the [136] modern gymnospermsand angiosperms. Gymnosperms produce "naked seeds" not fully enclosed in an ovary; modern representatives includeconifers, cycads, Ginkgo, and Gnetales. Angiosperms produce [137][138] seeds enclosed in a structure such as a carpel or anovary. Ongoing research on the molecular phylogenetics of living plants appears to show that the angiosperms are asister clade to the [139] gymnosperms.