Polyploidy-associated genome modifications during land plant evolution

Abstract

The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

“…These observations further support the notion that the ancestral teleost genome was rapidly reshaped with extensive rearrangements after the TGD. WGD-associated genomic rearrangement is also reported in angiosperms (2). Detailed analysis of the garpike genome is expected to provide a comprehensive view of the origin and early evolution of bony vertebrate genomes.…”

“…In particular, WGD events, known to have occurred in several major lineages of flowering plants (2), budding yeasts (3), and vertebrates (4) (Fig. 1A), are considered to have had a major impact on genomic architecture and consequently organismal features.…”

The legacy of diploid progenitors in allopolyploid gene expression patterns

“…Gottlieb ([2], p. 91) A common phenomenon in plant evolution is the hybridization of two diploid species, accompanied by whole-genome duplication, to produce an allotetraploid species with two homoeologous sub-genomes (see contributions by Soltis et al [3], Ramsey & Ramsey [4], Vanneste et al [5], Jiao & Paterson [6]). New allotetraploids contain duplicate copies of every gene that was present in both their parents.…”

Structural and functional divergence of homoeologous genes in allopolyploid plant genomes

“…Major food crops with sequenced genomes: rice (Goff et al, 2002), grape (Jaillon et al, 2007), maize (Schnable et al, 2009), cucumber (Huang et al, 2009), sorghum (Paterson et al, 2009), cacao (Argout et al, 2010), soybeen (Huang et al, 2010), apple (Velasco et al, 2010), cabbage (Wang et al, 2011a), strawberry (Shulaev et al, 2011), turnip (Wang et al, 2011b), potato (Xu et al, 2011), melon (GarciaMas et al, 2012, banana (D'Hont et al, 2012), tomato (The Tomato Genome Consortium, 2012), barley (Mayer et al, 2012); plum (Zhang et al, 2012), pear , watermelon , orange , peach (The International Peach Genome Initiative et al, 2013), beet (Juliane et al, 2013), chickpea (Varshney et al, 2013), cotton (Li et al, 2014), pepper (Kim et al, 2014), carrot (Iorizzo et al, 2016). ние), «межгеномный гетерозис» (за счет сочетания разных гомеоаллелей в полиплоидном ядре), а также приобрете-ние генами новых функций (Jiao et al, 2014). Известно, что полиплоидные формы чаще встречаются в районах с неблагоприятным климатом (Першина, 2009;Ekimova et al, 2012).…”