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.

Crop pangenomes

“…The genome sequence is the basis for a chromosome structure studying, a distribution of repetitive and coding sequences, and genes identification and annotation (Bragina et al, 2019). The different species genomes information allows a comparative phylogenetic analysis to study relationships among species, their origins, and evolutionary features (Marchant et al, 2016;Wendel et al, 2016). In agricultural plants, all these allows to assess the impact of a genetic variability on a gene function, to identify the genes responsible for the most valuable traits in crops (Schnable et al, 2009;Wing et al, 2018).…”

Post-zygotic reproductive isolation is not correlated with chromosome number in plants

“…pairs/groups of species used to estimate crossability index) were available for regressions on chromosome number, 99 samples for median Ks, and 31 samples for paleolog fraction. To account for potentially different patterns of diploidization in angiosperms and other plant clades [18], we further divided the dataset into 'angiosperms' and 'non-angiosperms. '…”

Plant and Animal Cytogenetics in Latin America

“…Polyploidy is a common phenomenon across numerous eukaryotic taxa (Soltis et al, 2014;Marchant et al, 2016) and is believed to play a significant role in the evolution of vascular plants (Otto and Whitton, 2000;. As many as 70-80% of Angiosperms, including many crop species, and up to 95% of Pteridophytes have a polyploid origin (Bennet, 2004;Gregory and Mable, 2005;Otto, 2007).…”