The Asymmetrical Evolution of the Mesopolyploid Brassica oleracea Genome

Tong, Chaobo; Kole, Chittaranjan; Liu, Lijiang; Cheng, Xiaohui; Huang, Junyan; S, Liu

doi:10.1007/978-3-030-31005-9_6

Cited by 3 publications

(3 citation statements)

References 41 publications

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“…3 ) even when only considering mutations that have arisen following the earliest allopolyploid diversification events, and correcting for removing the biases of unequal phylogenetic distances to each subgenome’s model progenitor diploid. Our work adds to a growing recognition that the two coresident subgenomes in cotton allopolyploids may be shaped asymmetrically by evolutionary processes, including interspecific introgression and selection under domestication ( Fang, Guan, et al 2017 ; Fang, Wang, et al 2017 ; Chen et al 2020 ; Yuan et al 2021 ), and that this phenomenon also extends to other important allopolyploid crop plants, including wheat ( Pont and Salse 2017 ; Jiao et al 2018 ) and Brassica ( Tong et al 2020 ).…”

Section: Discussionmentioning

confidence: 75%

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Conover

Wendel

2022

Molecular Biology and Evolution

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Whole genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1-2 million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two co-resident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g. dN/dS, πN/πS) may be biased when species of different ploidy levels are compared.

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Section: Discussionmentioning

confidence: 75%

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Conover

Wendel

2022

Molecular Biology and Evolution

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“…We found that the At subgenome of all species contains 2-3% more nonsynonymous mutations that are inferred to be deleterious (Figure 3) even when only considering mutations that have arisen following the earliest allopolyploid diversification events, and correcting for removing the biases of unequal phylogenetic distances to each subgenome’s model progenitor diploid. Our work adds to a growing recognition that the two co-resident subgenomes in cotton allopolyploids may be shaped asymmetrically by evolutionary processes, including interspecific introgression and selection under domestication (Fang, Wang, et al 2017; Fang, Guan, et al 2017; Chen et al 2020; Yuan et al 2021), and that this phenomenon also extends to other important allopolyploid crop plants, including wheat (Pont and Salse 2017; Jiao et al 2018) and Brassica (Tong et al 2020) .…”

Section: Discussionmentioning

confidence: 77%

Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally Between Subgenomes

Conover

Wendel

2021

Preprint

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Whole genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1-2 million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two co-resident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g. dN/dS, 𝛑N/𝛑S) may be biased when species of different ploidy levels are compared.

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“…We found that the At subgenome of all species contains 2-3% more nonsynonymous mutations that are inferred to be deleterious (Figure 4.5) even when only considering mutations that have arisen following the earliest allopolyploid diversification events, and correcting for removing the biases of unequal phylogenetic distances to each subgenome's model progenitor diploid. Our work adds to a growing recognition that the two coresident subgenomes in cotton allopolyploids may be shaped asymmetrically by evolutionary processes, including interspecific introgression and selection under domestication (Fang, Wang, et al 2017;Chen et al 2020;Yuan et al 2021), and that this phenomenon also extends to other important allopolyploid crop plants, including wheat (Pont and Salse 2017;Jiao et al 2018) and Brassica (Tong et al 2020).…”

Section: Asymmetry In Subgenomes In the Distribution Of Deleterious M...mentioning

confidence: 71%

Molecular evolution following allopolyploidization in Gossypium

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The Asymmetrical Evolution of the Mesopolyploid Brassica oleracea Genome

Cited by 3 publications

References 41 publications

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally Between Subgenomes

Molecular evolution following allopolyploidization in Gossypium

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