DOE Joint Genome Institute, Berkeley, CA, 94720, USA.
Estación Experimental de Aula Dei (EEAD-CSIC), Zaragoza, Spain.
Nat Commun. 2020 Jul 29;11(1):3670. doi: 10.1038/s41467-020-17302-5.
Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.
我们对多倍体基因组进化的理解受到限制，因为我们无法知道特定多倍体的确切起源。为了区分起源效应和多倍化后的进化，我们使用泛基因组方法研究了异源四倍体拟南芥及其二倍体祖先。比较分析表明，拟南芥杂种中大多数全基因存在/缺失的变异是其二倍体祖先中现存变异的一部分。对核单核苷酸变异、质体和与反转录转座子相关的 k- mers 的分析揭示了拟南芥杂种的两个独立起源，分别发生在约 140 万年前和 14 万年前。对年轻的拟南芥杂种系基因表达的研究表明，整个亚基因组表达没有偏向性。我们的结果与多倍化后基因组变化的逐渐积累以及亚基因组表达优势的缺乏相一致。重要的是，如果我们不使用泛基因组方法，我们将大大高估归因于多倍化后进化的基因组变化数量。
