Yang Jun, Xu Peng, Yu Diqiu
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Evol Bioinform Online. 2020 Sep 11;16:1176934320941495. doi: 10.1177/1176934320941495. eCollection 2020.
Rice () yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the gene family in japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, , and were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of genes in rice.
水稻（）产量与多种因素相关。转录调节因子是重要因素，例如典型的与节间缩短相关的序列（SRSs），其编码具有单个锌指基序的蛋白质。然而，关于水稻中该基因家族成员的进化和功能特征的知识并不充分。因此，我们对粳稻中的该基因家族进行了全基因组筛选和表征。我们还研究了来自11个水稻亚种的SRS蛋白，其中包括3个栽培品种、6个野生品种和2种其他基因组类型。还对玉米、高粱、和中的SRS成员进行了研究。通过系统发育分析评估，所有这些SRS蛋白均表现出物种特异性特征以及单子叶和双子叶特异性特征，基因结构和基序分析进一步验证了这一点。基因组比较表明，片段重复可能在该基因家族的重组及其表达水平中发挥了重要作用。该家族主要受到纯化选择压力。此外，表达数据表明该基因对各种非生物胁迫和激素处理有不同反应，表明它们的功能存在差异。我们的研究为阐明水稻中该基因的功能提供了很好的参考。
