Genome Evolution in Plants

Abstract

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. (2016) © 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. (2014) © Proceedings of the National Academy of Sciences.
Figure 4. Alternative splicing event types and rate in Arabidopsis, rice, maize and humans.
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Marchant, D Blaine, Soltis, Douglas E, and Soltis, Pamela S(Sep 2016) Genome Evolution in Plants. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0026814]