Zhu Siyuan, Tang Shouwei, Tan Zhijian, Yu Yongting, Dai Qiuzhong, Liu Touming
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
BMC Genomics. 2017 Jan 10;18(1):60. doi: 10.1186/s12864-016-3474-8.
Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported.
In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species. In addition, we identified orthologous genes and estimated their Ka and Ks values, in order to ascertain their selective pattern. Phylogenetic analysis based on the transcriptomes revealed that A. tuberosum was the most ancestral among the nine species, and analysis of orthologous genes between A. tuberosum and the other eight species indicated that 149 genes were subject to positive selection; whereas >3000 had undergone purifying selection in each species.
We found that many genes that are potentially related to programmed cell death either exhibited rapid diversification in fistular-leaved species, or were conserved in solid-leaved species in evolutionary history. These genes potentially involved in programmed cell death might play important roles in the formation of fistular leaf cavities in Allium, and the differing selection patterns in fistular- and solid-leaved species may be responsible for the evolution of fistular leaves.
葱属植物中常出现中空的叶片，先前的发育研究表明，中空叶片的形成过程涉及程序性细胞死亡。然而，关于程序性细胞死亡在中空叶片腔形成中作用的分子证据尚未见报道。
在本研究中，我们对9种葱属植物的叶片转录组进行了表征，其中包括6种中空叶和3种实心叶的物种。此外，我们鉴定了直系同源基因并估计了它们的Ka和Ks值，以确定它们的选择模式。基于转录组的系统发育分析表明，韭菜是这9个物种中最原始的，对韭菜与其他8个物种之间直系同源基因的分析表明，有149个基因受到正选择；而每个物种中有超过3000个基因经历了纯化选择。
我们发现，许多可能与程序性细胞死亡相关的基因要么在中空叶物种中表现出快速分化，要么在进化历史中在实心叶物种中保守。这些可能参与程序性细胞死亡的基因可能在葱属植物中空叶片腔的形成中起重要作用，中空叶和实心叶物种不同的选择模式可能是中空叶进化的原因。
