Cao Jun, Han Xi, Zhang Ticao, Yang Yongping, Huang Jinling, Hu Xiangyang
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
BMC Genomics. 2014 Dec 16;15(1):1116. doi: 10.1186/1471-2164-15-1116.
Vitis vinifera (grape) is one of the most economically significant fruit crops in the world. The availability of the recently released grape genome sequence offers an opportunity to identify and analyze some important gene families in this species. Subtilases are a group of subtilisin-like serine proteases that are involved in many biological processes in plants. However, no comprehensive study incorporating phylogeny, chromosomal location and gene duplication, gene organization, functional divergence, selective pressure and expression profiling has been reported so far for the grape.
In the present study, a comprehensive analysis of the subtilase gene family in V. vinifera was performed. Eighty subtilase genes were identified. Phylogenetic analyses indicated that these subtilase genes comprised eight groups. The gene organization is considerably conserved among the groups. Distribution of the subtilase genes is non-random across the chromosomes. A high proportion of these genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the subtilase gene family. Analyses of divergence and adaptive evolution show that while purifying selection may have been the main force driving the evolution of grape subtilases, some of the critical sites responsible for the divergence may have been under positive selection. Further analyses of real-time PCR data suggested that many subtilase genes might be important in the stress response and functional development of plants.
Tandem duplications as well as purifying and positive selections have contributed to the functional divergence of subtilase genes in V. vinifera. The data may contribute to a better understanding of the grape subtilase gene family.
葡萄是世界上经济意义最为重大的水果作物之一。最近公布的葡萄基因组序列为鉴定和分析该物种中的一些重要基因家族提供了契机。枯草杆菌蛋白酶是一类类似于枯草杆菌蛋白酶的丝氨酸蛋白酶，参与植物的许多生物学过程。然而，迄今为止尚未见针对葡萄开展的结合系统发育、染色体定位与基因复制、基因结构、功能分化、选择压力及表达谱分析的全面研究报道。
在本研究中，对葡萄中的枯草杆菌蛋白酶基因家族进行了全面分析。共鉴定出80个枯草杆菌蛋白酶基因。系统发育分析表明，这些枯草杆菌蛋白酶基因可分为八组。各组间基因结构相当保守。枯草杆菌蛋白酶基因在染色体上的分布并非随机。这些基因中有很大一部分优先聚集在一起，表明串联重复可能对枯草杆菌蛋白酶基因家族的扩张有显著贡献。对分化和适应性进化的分析表明，虽然纯化选择可能是驱动葡萄枯草杆菌蛋白酶进化的主要力量，但一些导致分化的关键位点可能受到了正选择。对实时PCR数据的进一步分析表明，许多枯草杆菌蛋白酶基因可能在植物的应激反应和功能发育中发挥重要作用。
串联重复以及纯化选择和正选择促成了葡萄中枯草杆菌蛋白酶基因的功能分化。这些数据可能有助于更好地理解葡萄枯草杆菌蛋白酶基因家族。
