关键词: 黄瓜, DIR, 基因家族, 生物信息学, 表达分析

Abstract: 【Objective】 Based on the cucumber genome information and transcriptome sequencing big-data, the DIR gene family in cucumber was identified with bioinformatics methods, and the expression pattern analysis of DIR family genes in different tissues and stresses response were analyzed. It will lay an important foundation for further study on the biological function of cucumber DIR genes. 【Method】 With the reported HMM model file of DIR gene, the probable DIR genes ID from the cucumber protein database was firstly identified using HMMSearch program in the HMMER software package. The cucumber DIR genes were ultimately verified using online tools Pfam and SMART. The tools of ExPASy, TBtools, GSDS, MEME, MEGA, MCScanX and Circos were used to analyze the physicochemical characteristics, chromosomal distributions, gene structure, phylogenetic tree and synteny of cucumber DIR genes. Based on cucumber transcriptome sequencing big-data of different tissues and under different stresses, transcriptome sequencing analysis was re-analyzed using cucumber V3 version genome information. The data of cucumber DIR genes in different transcriptome sequencing analysis were retrieved. The expression heatmaps of DIR gene family were drawn using TBtools softwore, and the expression patterns of cucumber DIR genes in different tissues and stresses response were analyzed. 【Result】 Total of 23 DIR genes were identified from cucumber genome, which distributed to 7 chromosomes. The number of amino acids of these DIR genes ranged from 78—684, and the molecular weight ranged from 8.70—73.82 kD. Phylogenetic analysis divided the cucumber DIR genes into 3 subgroups, the structure and motif of the genes in each subgroup were similar. Synteny analysis showed that the 12 cucumber DIR genes were collinearity with 19 Arabidopsis DIR genes with 27 kinds of linear relationships, and 12 cucumber DIR genes were collinearity with 11 rice DIR genes with 19 kinds of linear relationships. While only 8 cucumber DIR genes were conservative, which were not collinearity with any DIR gene in Arabidopsis and rice. Tissue-specific expression analysis revealed that some cucumber DIR genes have low or no expression levels in all tissues including root, stem, flower, fruit, leaf and so on, some cucumber DIR genes have high expression levels in all tissues, and some DIR genes have specific expression levels in some tissues, but no or low expression levels in other tissues. This suggested that different cucumber DIR genes have tissue specific expression patterns. The expression profiles analysis of cucumber DIR genes under biotic and abiotic stresses conditions revealed that cucumber DIR gene, CsaV3_4G023490, were up-regulated expression in response to all stresses, which means this gene play an important role in the process of cucumber growth and development. 【Conclusion】 Total of 23 DIR genes were identified in cucumber, which were divided into 3 subgroups. The gene members in each subgroup were highly conserved, the gene structure and protein conserved domain were different among 3 subgroups. The expression patterns of cucumber DIR genes in different tissues and stresses response were different, which coordinately regulated the growth and development of cucumber.

Key words: cucumber, DIR, gene family, bioinformatics, expression analysis