Evolutionary Genetics of Genome Merger and Doubling in Plants

Abstract

Polyploidy is a common mode of evolution in flowering plants. The profound effects of polyploidy on gene expression appear to be caused more by hybridity than by genome doubling. Epigenetic mechanisms underlying genome-wide changes in expression are as yet poorly understood; only methylation has received much study, and its importance varies among polyploids. Genetic diploidization begins with the earliest responses to genome merger and doubling; less is known about chromosomal diploidization. Polyploidy duplicates every gene in the genome, providing the raw material for divergence or partitioning of function in homoeologous copies. Preferential retention or loss of genes occurs in a wide range of taxa, suggesting that there is an underlying set of principles governing the fates of duplicated genes. Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages.

The genome of the domesticated apple (Malus × domestica Borkh.)

“…3). The rate of chromosome rearrangements after polyploidization (12 chromosome events in 60 My) is similar to that for poplar (~16 events in 60 My) 6 and lower than in maize (at least 17 chromosome fusion events in 5 My) 33 or in artificial neopolyploids 34 . In this sense, molecular clocks of perennial woody species seem slower than those of annual species, in terms of both nucleotide substitutions and chromosome rearrangements 9 .…”

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

“…A. suecica had a single origin at 12,000-300,000 years ago 41 . Combination of predominant cis effects between species and predominant trans effects during selfing might act in concert to provide opportunities for new allopolyploids to increase levels of adaptation and diversification during evolution 3,4 . A higher level of gene-expression divergence between F1 allotetraploids and A. suecica may suggest that many genes have diverged their expression over time.…”

“…I nterspecific hybridization and polyploidy occur in many flowering plants and some animals, leading to novel phenotypic variation [1][2][3][4][5] . Barbara McClintock 6 coined the term 'genome shock' to describe unprepared changes to cope with an existing programmed response in interspecific hybrids, leading to transposon activation and genomic instability.…”

“…The induced variation in the interspecific hybrids can be transmitted to the progeny if chromosomes are doubled to form stable allopolyploids 5,10 . Genome hybridization and polyploidization have had a pervasive role in the evolution and domestication of many flowering plants including the most important crops such as wheat, cotton and canola [2][3][4]10 .…”

High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex

“…Significantly, these rare unisexual animals are largely associated with polyploidy origin (Neaves and Baumann, 2011;Otto et al, 2007). In plants, polyploidy has been confirmed to be ubiquitous (Jiao et al, 2011), and polyploidy roles in increasing allelic diversity, altering genomic complexity, introducing novel traits, driving ecological transfiguration, and especially facilitating plant invasions have been suggested extensively (Doyle et al, 2008;Parisod et al, 2010;te Beest et al, 2012). Owing to the rarity of polyploid forms, the evolutionary consequence of polyploidy per se and the evolutionary potential of unisexual reproduction maintenance remain unknown in vertebrates.…”