Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat
Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat
复制标题
DOI：
10.1104/pp.112.205161
复制
发表时间：
2013-01-01
期刊：
影响因子：
7.4
通讯作者：
Gill, Bikram S.
中科院分区：
文献类型：
--
作者：
Akhunov, Eduard D.;Sehgal, Sunish;Gill, Bikram S.
全基因组复制（WGD）和二倍化的循环是真核基因组进化和物种形成的标志。多倍体小麦（Triticum aestivum）的基因组大小大幅增加，这主要归功于最近的全基因组测序。通过比较小麦和模式草基因组之间的基因结构变化模式、选择性剪接（AS）和密码子替换率，研究了这些过程如何影响基因进化的动态。在直系同源基因集中，在小麦中检测到的获得和丢失的外显子序列明显多于模式草。在小麦中，35% 的基因结构重排导致移码突变和提前终止密码子。与二穗短柄草相比，小麦谱系中 17% 的直向同源物的密码子突变率增加。在 38% 的表达基因中发现过早终止密码子与小麦基因组正在进行的假基因化是一致的。单个小麦亚基因组内的 AS 发生率 (21%-25%) 与二倍体植物相似。然而，我们发现基因复制的同源拷贝之间存在高度的 AS 模式差异。我们的结果与小麦谱系中 AS 亚型、非同义突变和基因结构重排的加速积累相一致，这可能是由于 WGD 产生的遗传冗余所致。尽管这些过程主要导致重复基因组的退化及其二倍化，但它们有可能促进新功能变异的起源，而这些变异在进化谱系中进行选择后，可能在新性状的起源中发挥重要作用。
Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%-25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.