Zhu Yan, Wu Ningning, Song Wanlu, Yin Guangjun, Qin Yajuan, Yan Yueming, Hu Yingkao
College of Life Sciences, Capital Normal University, Beijing 100048, China.
BMC Plant Biol. 2014 Apr 11;14:93. doi: 10.1186/1471-2229-14-93.
Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited.
A total of 75 expansin genes were identified in the soybean genome, and grouped into four subfamilies based on their phylogenetic relationships. Structural analysis revealed that the expansin genes are conserved in each subfamily, but are divergent among subfamilies. Furthermore, in soybean and Arabidopsis, the expansin gene family has been mainly expanded through tandem and segmental duplications; however, in rice, segmental duplication appears to be the dominant process that generates this superfamily. The transcriptome atlas revealed notable differential expression in either transcript abundance or expression patterns under normal growth conditions. This finding was consistent with the differential distribution of the cis-elements in the promoter region, and indicated wide functional divergence in this superfamily. Moreover, some critical amino acids that contribute to functional divergence and positive selection were detected. Finally, site model and branch-site model analysis of positive selection indicated that the soybean expansin gene superfamily is under strong positive selection, and that divergent selection constraints might have influenced the evolution of the four subfamilies.
This study demonstrated that the soybean expansin gene superfamily has expanded through tandem and segmental duplication. Differential expression indicated wide functional divergence in this superfamily. Furthermore, positive selection analysis revealed that divergent selection constraints might have influenced the evolution of the four subfamilies. In conclusion, the results of this study contribute novel detailed information about the molecular evolution of the expansin gene superfamily in soybean.
扩展蛋白是一类参与细胞膨大及多种其他发育过程的植物细胞壁松弛蛋白。扩展蛋白超家族包含四个亚家族，即α-扩展蛋白（EXPA）、β-扩展蛋白（EXPB）、类扩展蛋白A（EXLA）和类扩展蛋白B（EXLB）。尽管大豆的基因组测序已完成，但我们对大豆扩展蛋白基因的扩增模式和进化历史的了解仍然有限。
在大豆基因组中总共鉴定出75个扩展蛋白基因，并根据它们的系统发育关系分为四个亚家族。结构分析表明，扩展蛋白基因在每个亚家族中是保守的，但在亚家族之间存在差异。此外，在大豆和拟南芥中，扩展蛋白基因家族主要通过串联重复和片段重复进行扩增；然而，在水稻中，片段重复似乎是产生这个超家族的主要过程。转录组图谱显示，在正常生长条件下，转录本丰度或表达模式存在显著差异表达。这一发现与启动子区域顺式元件的差异分布一致，表明该超家族存在广泛的功能分化。此外，还检测到一些导致功能分化和正选择的关键氨基酸。最后，正选择的位点模型和分支位点模型分析表明，大豆扩展蛋白基因超家族受到强烈的正选择，并且不同的选择限制可能影响了四个亚家族的进化。
本研究表明，大豆扩展蛋白基因超家族通过串联重复和片段重复进行了扩增。差异表达表明该超家族存在广泛的功能分化。此外，正选择分析表明，不同的选择限制可能影响了四个亚家族的进化。总之，本研究结果为大豆扩展蛋白基因超家族的分子进化提供了新的详细信息。
