拟南芥和琴叶拟南芥中MADS-box基因的比较进化分析

Comparative evolutionary analysis of MADS-box genes in Arabidopsis thaliana and A. lyrata

MADS-box基因编码一类转录因子。在被子植物中,MADS-box基因对于营养生长和生殖发育都有重要的调控作用,是植物体(特别是花序、花和果实)的正常发育所不可或缺的。为了理解近缘物种在遗传基础上的异同,我们对拟南芥(Arabidopsis thaliana)和琴叶拟南芥(A.lyrata)基因组中MADS-box基因的拷贝数目和进化式样进行了比较分析。通过搜索公共数据库,我们在拟南芥和琴叶拟南芥中分别鉴定出了106和115个基因。系统发育分析的结果表明,这些基因属于I型和II型MADS-box基因。在两个物种分化之后,II型基因的拷贝数目变化不大,I型基因则经历了多次独立的基因丢失和获得事件。通过比较这些基因在染色体上的排列,我们不但鉴定出了存在微共线性的基因组区段,而且发现新基因产生的主要机制是串联重复和散在重复。分子进化的研究进一步表明,I型和II型基因在进化式样上存在着显著差异:II型基因在进化中一般都受到了较强的选择压力,而I型基因大多受到的选择压力较弱。本研究将为深入理解近缘物种在基因和基因组层面上的异同、探讨物种分化和生物多样性形成的机制等问题提供新思路。

MADS-box genes encode a family of transcription factors. In angiosperms, MADS-box genes play key roles in vegetative growth and reproductive development, and are indispensable for the formation of inflorescences, flowers and fruits. To understand the evolution of MADS-box genes on a relatively small time scale, we conducted comparative genomic studies of a pair of closely related plant species, Arabidopsis thaliana and A. lyrata. A total of 106 and 115 MADS-box genes were identified from the two species, respectively, and phylogenetic analyses suggested that these genes correspond to Types I and II MADS-box genes. Type I genes have been duplicated and lost extensively in the lineages leading to the two species, whereas the number of Type II genes has not changed very much during the same period. Comparisons of the locations of orthologous gene pairs not only detected chromosomal regions that showed clear microsynteny between the two genomes, but also found evidence that most newly gained genes were generated through tandem and dispersed duplications rather than segmental duplication. Molecular evolutionary studies further suggested that different clades of MADS-box genes have experienced significantly different patterns of evolution, with functional constraints being less stringent for Type I genes than for Type II genes. Our results will help better understand the genetic differences between closely related species, and stimulate additional studies on the mechanisms that underlie speciation and biodiversification.