Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus.
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus.
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重放进化磁带以研究异源多倍体甘蓝型油菜的亚基因组优势
DOI：
10.1111/nph.17137
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发表时间：
2021-04
期刊：
影响因子：
--
通讯作者：
Edger PP
中科院分区：
文献类型：
--
作者：
Bird KA;Niederhuth CE;Ou S;Gehan M;Pires JC;Xiong Z;VanBuren R;Edger PP
异源多倍化将进化上截然不同的亲本基因组(亚基因组)合并成一个核。一种常见的观察是，一个亚基因组比另一个亚基因组“占优势”，通常表达得更高。在这里，我们用6个等基因重新合成的甘蓝型油菜异源多倍体品系‘重播了进化磁带’，并研究了多倍化后前10代的亚基因组显性模式。我们发现，相同的亚基因组在所有品系和世代中的表达一直更占优势，并且70%的偏向基因对在所有品系和双亲的电子杂交中显示出相同的显性模式。基因网络分析表明，甘蓝亚基因组偏向对具有丰富的网络相互作用和多种生物学功能，而甘蓝亚基因组偏向对没有发现富集性。此外，亚基因组之间的DNA甲基化差异反映了在所有品系和世代中观察到的对显性亚基因组的基因表达偏向。当比较祖先基因组时，也发现了许多基因表达和甲基化的差异，这表明亚基因组优势部分与亲本基因组差异有关，而不仅仅是异源多倍化的副产品。这些发现表明，在异源多倍体中‘重播进化磁带’会导致在很大程度上可重复和可预测的亚基因组表达优势模式。
Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is ‘dominant’ over the other subgenome, often being more highly expressed. Here, we ‘replayed the evolutionary tape’ with six isogenic resynthesised Brassica napus allopolyploid lines and investigated subgenome dominance patterns over the first 10 generations postpolyploidisation. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea subgenome biased pairs, but no enrichment was identified for Brassica rapa subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the dominant subgenome in all lines and generations. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting that subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidisation. These findings demonstrate that ‘replaying the evolutionary tape’ in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns.
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