Patterns and impacting factors of gene evolutionary rate between wild and cultivated emmer wheat (Triticum turgidum)
Patterns and impacting factors of gene evolutionary rate between wild and cultivated emmer wheat (Triticum turgidum)
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DOI：
10.1111/jse.12852
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发表时间：
2022-04
影响因子：
3.7
通讯作者：
Pengzheng Lei;Qi Ai;Zhu Xiong;Jianan Lu;Xiaoqiang Wei;S. Weining;Xiaoqin Liu;Xiaojun Nie
中科院分区：
文献类型：
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作者：
Pengzheng Lei;Qi Ai;Zhu Xiong;Jianan Lu;Xiaoqiang Wei;S. Weining;Xiaoqin Liu;Xiaojun Nie
四倍体二粒小麦（Triticum turgidum L.，BBAA是面包小麦的始祖，为小麦的改良提供了宝贵的遗传资源和基因库。然而，四倍体小麦的进化轨迹，特别是不同类型基因的进化命运还没有得到很好的研究。在本研究中，通过在全基因组和亚基因组水平上比较野生二粒小麦和栽培硬粒小麦之间的直系同源物，计算非同义替换率（dN）和同义替换率（dS），以获得正选择基因（PSG）和负选择基因（NSG）。然后，对PSG和NSG的突变率、基因长度、外显子数目、GC含量、密码子偏好性和表达水平进行了全面的调查和比较。在野生二粒小麦和栽培硬粒小麦中，位于A和B亚基因组之间的PSG基因长度和外显子数目均比非PSG短，而从野生二粒小麦到栽培硬粒小麦，PSG基因长度和外显子数目均比非PSG长。此外，与NSG相比，PSG显示出更高的表达水平和更强的密码子使用偏好，但遗传多样性较低。最后，发现两个PSG TdER 1 - 6 B和TdLC 7 - 2A分别在调节四倍体小麦的粒宽和株高中起关键作用。本研究系统地研究了四倍体小麦中PSGs和NSGs在进化、结构和功能上的差异，有助于更好地理解小麦驯化和进化过程中的选择模式和进化轨迹。
Tetraploid emmer wheat (Triticum turgidum L., BBAA) is the founder progenitor of bread wheat, providing the valuable genetic resource and gene pool for wheat improvement. However, the evolutionary trajectory of tetraploid wheat, especially the evolutionary fate of different types of genes has not been well studied. In this study, the rate of non‐synonymous substitution (dN) and synonymous substitution (dS) was calculated by comparing the orthologs between the wild emmer and cultivated durum wheat at the whole genome and subgenome levels to obtain the positively selected genes (PSGs) and negatively selected genes (NSGs). Then, mutation rate, gene length, exon number, GC content, codon bias, and expression level were comprehensively investigated and compared between the PSGs and NSGs. Within both wild emmer and cultivated durum wheat, PSGs between A and B subgenome displayed shorter gene and exon lengths as well as fewer exon numbers compared with NSGs, whereas from wild emmer to cultivated durum wheat, PSGs showed longer gene length and more exon numbers. Furthermore, PSGs displayed much higher expression levels and stronger codon usage bias, but lower genetic diversity compared with NSGs. Finally, two PSGs TdER1‐6B, and TdLC7‐2A, were found to play the crucial roles in regulating grain width and plant height of tetraploid wheat, respectively. This study systematically investigated the evolutionary, structural, and functional difference between PSGs and NSGs in tetraploid wheat, which will contribute to a better understanding of the selective mode and evolutionary trajectory during wheat domestication and evolution.