Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication
Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication
复制标题
全基因组复制后水稻Dof基因复制成员的古代快速功能分化和固定
DOI：
10.1111/tpj.15516
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Traw MB
中科院分区：
文献类型：
--
作者：
Yu L;Ma S;Zhang X;Tian D;Yang Sihai;jia X;Traw MB
植物的全基因组复制(WGD)通常伴随着基因组的缩小，即新基因组的大部分丢失。这种缩小是伴随着剩余基因进化率的提高还是降低，目前还知之甚少，尤其是因为同源基因配对经常被染色体重排所掩盖。在这里，我们使用新发表的莎草基因组，命名为Kobresia littledalei，和CRISPR/Cas-9编辑来研究7000万年前的Rho WGD事件(MYA)如何影响水稻和高粱的转录因子进化速度、命运和功能。由于这两种作物在农学上的重要性，我们重点研究了这两种作物中与一个锌指(DOF)转录因子家族的30个成员的DNA结合。利用Kobresia(97 MYA)和高粱(50 MYA)的已知物种形成日期，我们发现在WGD之后的2000万年期间，关键DOF结构域的氨基酸替代率比WGD前后高出一倍以上。通过同步性块的比较，我们报告了至少11%的Dofgene在70到50 MYA期间被清除，而在最近的5000万年间隔内只有6%的Dofgene丢失。CRISPR/Cas9编辑揭示了开花过程中普遍存在的与适合度相关的缺陷和配对成员缺乏冗余，以及基因对之间表达的显著差异。总而言之，这些发现证明了Dofgene作为深入进化研究的模型的力量，并提供了迄今为止关于Rho WGD对基因谱系影响的最详细的描述之一。
Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namelyKobresia littledalei, and CRISPR/Cas‐9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30‐member DNA‐binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice fromKobresia(97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20‐million‐year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% ofDofgenes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50‐million‐year interval. CRISPR/Cas9 editing revealed widespread fitness‐related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength ofDofgenes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.