4种模式植物LRR VIII-2亚家族基因的鉴定和进化历史分析

全基因组重复与串联重复是发生基因重复的重要机制, 也是基因组和遗传系统多样化的重要动力。LRR-RLK编码富含亮氨酸重复的类受体蛋白激酶, 是被子植物进化史上发生大规模扩张而形成的多基因家族。拟南芥(Arabidopsis thaliana) AtLRR-RLK包含15个亚家族, AtLRR VIII-2是其中发生串联重复比例最高的亚家族。通过分析拟南芥、杨树(Populus trichocarpa)、葡萄(Vitis vinifera)和番木瓜(Carica papaya) 4种模式植物中LRR VIII-2亚家族基因的扩张及差异保留情况, 结果显示, LRR VIII-2在杨树中的扩张程度最高, 在拟南芥和葡萄中的扩张程度居中, 但在番木瓜中发生丢失。拟南芥、杨树和葡萄LRR VIII-2亚家族具有旁系同源基因对, 但在番木瓜中未发现旁系同源基因。除杨树中的1对旁系同源基因外, 4种模式植物中LRR VIII-2亚家族的旁系和直系同源基因都受到较强的纯化选择作用。对LRR VIII-2亚家族进化历史的深入分析有助于理解基因重复在植物进化中的作用和意义, 可为预测同源基因功能及解析其它基因家族进化历史提供参考。

Identification and Evolution of LRR VIII-2 Subfamily Genes in Four Model Plant Species

Whole-genome duplication and tandem duplication are two important mechanisms for gene duplication, which play important roles in promoting the genomic and genetic diversity. In Arabidopsis, AtLRR-RLK encodes receptor-like kinases rich in leucine repeats, which is a multi-gene family arising from large-scale gene expansion during angiosperm evolution. It is composed of 15 subfamilies, among which, AtLRR VIII-2 is the subfamily with the highest proportion of tandem repeats. In this study, we use the genes in LRR VIII-2 as an example to analyze the gene expansion and differential retention in four model plants (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Carica papaya). Results showed that paralogous gene pairs were identified in the LRR VIII-2 subfamily in Arabidopsis, poplar and grape, while no such pair was found in papaya. The LRR VIII-2 subfamily expanded the most significantly in poplar and moderately expanded in Arabidopsis and grape, but some genes of the LRR VIII-2 subfamily in papaya have been lost. In addition, the paralogous and orthologous genes in the LRR VIII-2 subfamily were under strong purifying selection in the four investigated plant species, except for a pair of paralogous genes in poplar. An in-depth phylogenetic analysis of the LRR VIII-2 subfamily helps to understand the role and significance of gene duplication in plant evolution, and provides useful information for predicting the function of homologous gene among different species. This analytical pipeline is also applicable for deciphering the evolution history of other gene families.