Genome Evolution in Plants


The genomes of land plants vary dramatically in size and chromosome number, and ongoing studies are clarifying the processes that shape their composition, structure and function. Polyploidy produces an entirely duplicated genome where the processes of nonfunctionalisation, subfunctionalisation and neofunctionalisation occur at individual loci or across entire genetic pathways, with both short‐ and long‐term effects. Transposable elements mould and alter genomes via a wide array of direct and indirect mechanisms extending well beyond their capacity to move throughout genomes. Horizontal gene transfer affects genome evolution of a lineage by incorporating novel genetic material from a separate lineage. Alternative splicing results in the inclusion and exclusion of a gene's exons and introns in processed messenger ribonucleic acid, altering the amino acid sequence and increasing an organism's protein repertoire without altering gene number. The impacts of these processes on plant genome evolution are just beginning to emerge as nonmodel genomes are sequenced.

Key Concepts

  • Polyploidy, or whole‐genome duplication, can result in immediate genomic and genetic variation.
  • Gene retention or loss following polyploidy may depend on gene function and expression levels.
  • Transposable elements can actively or passively alter genome composition and genetic networks via a variety of processes.
  • Horizontal gene transfer has been most commonly found in plant mitochondrial genomes, although more cases are being found in nuclear genomes.
  • Alternative splicing can provide multiple gene products from a single nucleotide sequence.
  • The conservation and evolutionary significance of alternative splicing patterns are just beginning to be elucidated in plants.
  • Genome size in plants varies from among the smallest eukaryotic genomes to the largest eukaryotic genomes yet determined.

Keywords: polyploidy; whole‐genome duplication; horizontal gene transfer; transposable elements; alternative splicing; plant evolution; genome size

Figure 1. The two types of polyploidy: allopolyploidy and autopolyploidy. Allopolyploidy is the merger and duplication of genomes from two (or more) different species. Autopolyploidy is genome doubling within a single species.
Figure 2. The phases of genome evolution following polyploidisation to diploidisation. Reproduced with permission from Soltis et al. () © The Botanical Society of America.
Figure 3. The composition and phylogeny of fern neochrome. (a) The neochrome gene is a chimera of phytochrome and phototropin genes. (b) Phylogeny of neochrome and phototropin across green plants. Hypothesised HGT event is labelled. From Li et al. () © Proceedings of the National Academy of Sciences.
Figure 4. Alternative splicing event types and rate in Arabidopsis, rice, maize and humans.


Albertin W and Marullo P (2012) Polyploidy in fungi: evolution after whole‐genome duplication. Proceedings of the Royal Society of London B: Biological Sciences 279: 2497–2509.

Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.

Barbazuk WB, Fu Y and McGinnis KM (2008) Genome‐wide analyses of alternative splicing in plants: opportunities and challenges. Genome Research 18: 1381–1392.

Barker MS, Vogel H and Schranz ME (2009) Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biology and Evolution 1: 391–399.

Bennett MD, Leitch IJ (2012) Plant DNA C‐values Database (release 6.0, Dec 2012). (accessed 20 July 2016).

Bennetzen JL, Ma J and Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95: 127–132.

Birol I, Raymond A, Jackman SD, et al. (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole‐genome shotgun sequencing data. Bioinformatics 29 (12): 1492–1497.

Blanc G and Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. The Plant Cell 16: 1667–1678.

Braasch I and Postlethwait JH (2012) Polyploidy in fish and the teleost genome duplication. In: Soltis PS and Soltis DE (eds) Polyploidy and Genome Evolution, pp. 341–383. Berlin/Heidelberg: Springer.

Brandt J, Schrauth S, Veith AM, et al. (2005) Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon‐derived neogenes in mammals. Gene 345: 101–111.

Brosius J (2003) The contribution of RNAs and retroposition to evolutionary novelties. In: Long M (ed.) Origin and Evolution of New Gene Functions, pp. 99–116. Dordrecht: Springer.

Chamala S, Feng G, Chavarro C and Barbazuk WB (2015) Genome‐wide identification of evolutionarily conserved alternative splicing events in flowering plants. Frontiers in Bioengineering and Biotechnology 3: 33.

Conant GC, Birchler JA and Pires JC (2014) Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology 19: 91–98.

Crow KD and Wagner GP (2006) What is the role of genome duplication in the evolution of complexity and diversity? Molecular Biology and Evolution 23: 887–892.

Davis CC and Xi Z (2015) Horizontal gene transfer in parasitic plants. Current Opinion in Plant Biology 26: 14–19.

De La Torre AR, Birol I, Bousquet J, et al. (2014) Insights into conifer giga‐genomes. Plant Physiology 166: 1724–1732.

De Smet R, Adams KL, Vandepoele K, et al. (2013) Convergent gene loss following gene and genome duplications creates single‐copy families in flowering plants. Proceedings of the National Academy of Sciences 110: 2898–2903.

Devos KM, Brown JKM and Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Research 12: 1075–1079.

Evans BJ, Pyron RA and Wiens JJ (2012) Polyploidization and sex chromosome evolution in amphibians. In: Soltis PS and Soltis DE (eds) Polyploidy and Genome Evolution, pp. 385–410. Berlin, Heidelberg: Springer.

Feschotte C, Jiang N and Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nature Reviews. Genetics 3: 329–341.

Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nature Reviews. Genetics 9: 397–405.

Force A, Lynch M, Pickett FB, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531–1545.

Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole‐genome, segmental, or by transposition. Annual Review of Plant Biology 60: 433–453.

Gaeta RT, Pires JC, Iniguez‐Luy F, et al. (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. The Plant Cell 19: 3403–3417.

Gurdon C, Svab Z, Feng Y, et al. (2016) Cell‐to‐cell movement of mitochondria in plants. Proceedings of the National Academy of Sciences 113: 3395–3400.

Jiao Y, Wickett NJ, Ayyampalayam S, et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97–100.

Jiao Y, Leebens‐Mack J, Ayyampalayam S, et al. (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: R3.

Jurka J (2004) Evolutionary impact of human Alu repetitive elements. Current Opinion in Genetics & Development 14: 603–608.

Kim G, LeBlanc ML, Wafula EK, et al. (2014) Genomic‐scale exchange of mRNA between a parasitic plant and its hosts. Science 345: 808–811.

Le QH, Wright S, Yu Z, et al. (2000) Transposon diversity in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 97: 7376–7381.

Lewis WH (ed.) (1980) Polyploidy. Boston, MA: Springer.

Li FW, Villarreal JC, Kelly S, et al. (2014) Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences 111: 6672–6677.

Li Z, Baniaga AE, Sessa EB, et al. (2015) Early genome duplications in conifers and other seed plants. Science Advances 1: e1501084.

Lockton S and Gaut BS (2009) The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. Journal of Molecular Evolution 68: 80–89.

Lynch M and Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155.

Mandadi KK and Scholthof KB (2015) Genome‐wide analysis of alternative splicing landscapes modulated during plant‐virus interactions in Brachypodium distachyon. The Plant Cell 27: 71–85.

Matzke MA and Mosher RA (2014) RNA‐directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews. Genetics 15 (6): 394–408.

McLysaght A, Hokamp K and Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nature Genetics 31: 200–204.

Naito K, Zhang F, Tsukiyama T, et al. (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130–1134.

Nystedt B, Street NR, Wetterbom A, et al. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579–584.

Ohno S (1970) Evolution by gene and genome duplication. Berlin: Springer.

Oliver KR and Greene WK (2009) Transposable elements: powerful facilitators of evolution. BioEssays 31: 703–714.

Paterson AH, Chapman BA, Kissinger JC, et al. (2006) Many gene and domain families have convergent fates following independent whole‐genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends in Genetics 22: 597–602.

Paterson AH, Bowers JE, Bruggmann R, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556.

Piegu B, Guyot R, Picault N, et al. (2006) Doubling genome size without polyploidization: dynamics of retrotransposition‐driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research 16: 1262–1269.

Reddy AS (2007) Alternative splicing of pre‐messenger RNAs in plants in the genomic era. Annual Review of Plant Biology 58: 267–294.

Rice DW, Alverson AJ, Richardson AO, et al. (2013) Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342: 1468–1473.

Rice A, Glick L, Abadi S, et al. (2015) The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers. New Phytologist 206: 19–26.

Richardson AO and Palmer JD (2007) Horizontal gene transfer in plants. Journal of Experimental Botany 58: 1–9.

Schnable PS, Ware D, Fulton RS, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–1115.

Selmecki AM, Maruvka YE, Richmond PA, et al. (2015) Polyploidy can drive rapid adaptation in yeast. Nature 519: 349–352.

Soltis DE and Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends in Ecology & Evolution 14: 348–352.

Soltis DE, Albert VA, Leebens‐Mack J, et al. (2009) Polyploidy and angiosperm diversification. American Journal of Botany 96: 336–348.

Soltis DE, Buggs RJ, Barbazuk WB, et al. (2012) The early stages of polyploidy: rapid and repeated evolution in Tragopogon. In: Soltis PS and Soltis DC (eds) Polyploidy and Genome Evolution, pp. 271–292. Berlin Heidelberg: Springer.

Soltis DE, Visger CJ, Marchant DB, et al. (2016) Polyploidy: pitfalls and paths to a paradigm. American Journal of Botany 103: 1146–1166.

Stebbins GL (1950) Variation and Evolution in Plants. New York: Columbia University Press.

Stegemann S and Bock R (2009) Exchange of genetic material between cells in plant tissue grafts. Science 324: 649–651.

Sterck L, Rombauts S, Vandepoele K, et al. (2007) How many genes are there in plants (… and why are they there)? Current Opinion in Plant Biology 10: 199–203.

Tang H, Bowers JE, Wang X, et al. (2008) Synteny and collinearity in plant genomes. Science 320: 486–488.

Tang H, Bowers JE, Wang X, et al. (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proceedings of the National Academy of Sciences 107: 472–477.

Tank DC, Eastman JM, Pennell MW, et al. (2015) Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. The New Phytologist 207: 454–467.

Vision TJ, Brown DG and Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114–2117.

Wang W, Zheng H, Fan C, et al. (2006) High rate of chimeric gene origination by retroposition in plant genomes. The Plant Cell 18: 1791–1802.

Wang J, Guo H, Jin D, et al. (2015) Comparative analysis of gene conversion between duplicated regions in Brassica rapa and B. oleracea genomes. In: Wang W and Kole C (eds) The Brassica rapa Genome, pp. 121–129. Berlin, Heidelberg: Springer.

Wood TE, Takebayashi N, Barker MS, et al. (2009) The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences 106: 13875–13879.

Xiong Z, Gaeta RT and Pires JC (2011) Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proceedings of the National Academy of Sciences of the United States of America 108: 7908–7913.

Yoo MJ, Liu X, Pires JC, et al. (2014) Nonadditive gene expression in polyploids. Annual Review of Genetics 48: 485–517.

Zhang J and Peterson T (2004) Transposition of reversed Ac element ends generates chromosome rearrangements in maize. Genetics 167: 1929–1937.

Zimin A, Stevens KA, Crepeau MW, et al. (2014) Sequencing and assembly of the 22‐gb loblolly pine genome. Genetics 196: 875–890.

Further Reading

Bergthorsson U, Richardson AO, Young GJ, et al. (2004) Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proceedings of the National Academy of Sciences of the United States of America 101: 17747–17752.

Bock R (2010) The give‐and‐take of DNA: horizontal gene transfer in plants. Trends in Plant Science 15: 11–22.

Doyle JJ, Flagel LE, Paterson AH, et al. (2008) Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics 42: 443–461.

Lim KY, Soltis DE, Soltis PS, et al. (2008) Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS One 3: e3353.

Reddy AS, Marquez Y, Kalyna M, et al. (2013) Complexity of the alternative splicing landscape in plants. The Plant Cell 25: 3657–3683.

Sankoff D (2001) Gene and genome duplication. Current Opinion in Genetics & Development 11: 681–684.

Schnable JC, Springer NM and Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences of the United States of America 108: 4069–4074.

Soltis PS, Liu X, Marchant DB, Visger CJ, et al. (2014) Polyploidy and novelty: Gottlieb's legacy. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 369 (1648: pii: 20130351).

Soltis PS, Marchant DB, Van de Peer Y, et al. (2015) Polyploidy and genome evolution in plants. Current Opinion in Genetics & Development 35: 119–125.

Wendel JF (2015) The wondrous cycles of polyploidy in plants. American Journal of Botany 102: 1753–1756.

Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proceedings of the National Academy of Sciences 103: 17600–17601.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Marchant, D Blaine, Soltis, Douglas E, and Soltis, Pamela S(Sep 2016) Genome Evolution in Plants. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0026814]