Gradual evolution of allopolyploidy in Arabidopsis suecica.
Gradual evolution of allopolyploidy in Arabidopsis suecica.
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DOI：
10.1038/s41559-021-01525-w
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发表时间：
2021-10
影响因子：
16.8
通讯作者：
Nordborg M
中科院分区：
文献类型：
--
作者：
Burns R;Mandáková T;Gunis J;Soto-Jiménez LM;Liu C;Lysak MA;Novikova PY;Nordborg M
大多数二倍体生物都有多倍体祖先。多倍化的进化过程知之甚少，但经常被猜测涉及某种形式的基因组休克，如基因组重组和亚基因组表达优势。在这里，我们研究了拟南芥的多倍化，这是一种冰川后的异源多倍体物种，由拟南芥和拟南芥杂交而成。我们建立了一个染色体水平的甘蔗基因组组合，并用来自所有物种的多态和转录组数据对其进行补充。尽管在大约600万年前(Ma)，祖先物种之间存在差异，并且他们的基因组组成也不同，但我们没有看到基因组冲击的证据：猪链霉菌基因组与祖先基因组共线；在表达上没有亚基因组优势；转座子动态似乎是稳定的。然而，我们发现了一些变化，表明它们逐渐适应多倍体。具体地说，拟南芥的亚基因组表现出减数分裂相关基因的上调，这可能是为了防止在人工合成的拟南芥中观察到的非整倍体和不希望看到的同源交换，而花生亚基因组表现出细胞核过程的上调，这可能是对新的细胞质环境的响应，其中的质体是从拟南芥遗传过来的。这些变化在合成杂交种中看不到，因此很可能代表着随后的进化。拟南芥是由拟南芥和拟南芥杂交而成的天然异源四倍体物种。对基因组和转录组数据的比较分析表明，没有证据表明大豆与结构和功能变化有关的主要基因组变化，但揭示了减数分裂机制和细胞-核过程的变化。
Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution. Arabidopsis suecica is a natural allotetraploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. Comparative analysis of genome and transcriptome data shows no evidence for major genomic changes linked to structural and functional alterations in A. suecica but reveals changes to the meiotic machinery and cyto-nuclear processes.
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