棉花CLE多肽家族的全基因组鉴定与生物信息学分析

Genome-Wide Identification and Characterization of CLE Family in Cotton(Gossypium spp.)

【目的】CLE(CLAVATA3/Embryo surrounding region-related)多肽是一类小分子分泌蛋白,在植物生长发育过程中,对于维持分生组织细胞增殖与分化间的平衡起到重要的信号转导和调控作用。CLE家族是迄今为止报道的最大的植物多肽分子家族,也是近十年来研究最为热门的植物多肽激素。尽管CLE基因家族在拟南芥和水稻等模式植物中取得较多的研究进展,但在棉花中有关CLE多肽基因家族的研究尚属空白。通过对CLE多肽家族的鉴定及演化研究,可以为进一步挖掘棉花中的功能多肽及其信号转导研究提供一定的理论基础。【方法】本文以亚洲棉(Gossypium arboreum L.)、雷蒙德氏棉(G. raimondii Ulbrich)、陆地棉(G. hirsutum L.)和海岛棉(G. barbadense L.)为研究对象,利用生物信息学方法和已鉴定的拟南芥CLE基因序列,在棉花基因组中进行同源比对,并对4个棉种中的CLE家族成员进行全基因组鉴定和分析。【结果】共得到148个棉花CLE候选基因。陆地棉和海岛棉中CLE基因数量都分别是亚洲棉和雷蒙德氏棉的2倍。聚类分析将所有CLE基因分为5个亚组。Ka/Ks分析表明大部分基因都经历了负选择作用,有11对基因经历了显著的正选择作用。转录组数据分析发现,除海岛棉中的GbCLE39、GbCLE13、GbCLE43,陆地棉中GhCLE34、GhCLE9以及亚组棉中的GaCLE4外,大部分CLE基因在棉花组织中的表达量较低,这与多肽在植物体内含量较低相一致。CLE核心保守基序分析发现了12个棉花特有的多肽,其中有2个多肽来源于受到强烈正选择作用的基因,因此在后续研究中可以对其进行进一步深入分析。【结论】本文利用生物信息学、比较基因组学等方法,首次对棉花的CLE基因家族进行了鉴定和分析,对于进一步挖掘棉花中的功能多肽及其信号调控网络研究提供了一定的理论基础。

[Objective] CLE (CLAVATA3/Embryo surrounding region-related), a class of small secreted protein, plays an important role in sustaining the balance between cell proliferation and differentiation during the progress of plant growth and development. CLE gene family is the largest peptide family which has been identified so far, and it is also the hotspot of plant peptide studies. Although the study of CLE has made a great progress in Arabidopsis and rice, the CLE peptides in cotton have rarely been studied. Genome-wide analysis of CLE peptides in cotton will helpful to understand the evolutionary history and the regulation mechanism of peptides in cotton.[Method] In this study, we identified the members of CLE peptide family in the genomes of four cotton species using bioinformatics methods.[Result] One hundred and forty-eight CLE genes were identified in the four cotton species. The number of CLE gene in Gossypium hirsutum L. and G. barbadense L. are twice as much as in both G. arboreum and G. raimondii, respectively. These genes were divided into five clusters by phylogenetic analysis. The Ka/Ks ratios of most orthologs were less one, suggesting that most genes likely underwent purifying selection. We also detected eleven homologous gene pairs under positive selection. Using online published transcriptome data, we found that most CLE genes were expressed at low levels, and only six genes (GhCLE34, GhCLE9, GaCLE4, GbCLE39, GbCLE13, and GbCLE43) showed relatively high expression level. The conserved motif analysis showed that there are 12 specific CLE peptides in cotton, two of which derived from genes that under positive selection, which should be paid more attention in the future study.[Conclusion] Using bioinformatics methods and comparative genomics, we identified and characterized the CLE genes in cotton. These results may be useful for future studies of functions and regulation mechanism of CLE peptides in cotton.