Abstract:

【Objective】The objectives of this research were to identify the Homeodomain-Leucine Zipper (HD-Zip) family genes from pepper (Capsicum annuum) genome, to know the profile of HD-Zip family such as gene number, gene distribution, gene structure, evolutionary process and expression patterns in different tissues, and to provide theoretical basis for exploring what roles the HD-Zips play in pepper. 【Method】HD-Zip genes in pepper genome were identified by BLAST software based on HD-Zip from Arabidopsis, and verified by Pfam and SMART software. EMBOSS Programs, MEGA, GSDS, MEME, MCScanX, OrthoMCL and Circos softwares were used for bioinformatics analysis of HD-Zip protein and gene sequences. Expression patterns and gene co-regulatory network were analyzed by R and Cytoscape software. 【Result】Total of 42 HD-Zip genes were identified from ‘Zunla-1’ pepper genome, named as CaHDZ01-CaHDZ42. The length of their coding sequences ranged from 459 to 2 529 bps, and the isoelectric point of 70% CaHDZs was less than 7.0. The analysis of the gene’s location on the chromosome revealed that CaHDZs were unevenly distributed on 12 chromosomes of the pepper, except for CaHDZ42. The gene family could be divided into four subgroups, containing 18, 9, 5 and 10 CaHDZ genes, respectively. There were significant differences in gene structure and protein conserved domains among the subgroups. The number of orthologs among pepper, tomato and Arabidopsis was almost the same, but there were a little more orthologs between pepper and tomato. While the number of paralogs in Arabidopsis was significantly more than that in tomato and pepper, and the least in pepper, suggesting that the number of CaHDZ genes did not increase significantly along with genomic replication. To further understand the evolutionary history of CaHDZs in plant, HD-Zip homologous genes in Arabidopsis and 8 other plant species were analyzed. The results showed that all the major subgroups of HD-Zips existed in angiosperms. It was inferred that HD-Zip genes were divided into two groups initially. Then, one group differentiated into subgroup I and II, and the other differentiated into subgroups III and IV. The results of expression patterns analysis showed that the expression trends of four subgroups were different. Most of subgroup I genes expressed highly in pepper, such as CaHDZ22, and the expression of which was highest in stem, suggesting that this gene might play an important role in the growth of pepper stem. The expressions of subgroups II, III and IV CaHDZs were relatively low, but some of them expressed highly in specific tissues. For example, the expression of CaHDZ34 was high in late ripening stage of pepper fruits, CaHDZ02 and CaHDZ28 expressed highly in fruit enlargement stage, and CaHDZ04 expressed highly in early ripening stage of pepper fruits. In the coregulatory networks of CaHDZs, the Pearson correlation coefficients (PCCs) of 33 pairs of CaHDZs were greater than 0.8, and 6 pairs were greater than 0.9, suggesting that the CaHDZs coordinated the growth and development in pepper, and there were cooperative interactions among subgroups. 【Conclusion】All of 42 HD-Zip gene family members were identified from the ‘Zunla-1’ pepper genome, which could be divided into four subgroups. During the evolutionary history, CaHDZs were highly conservative and expanded slowly. Subgroup I and subgroup II had a closer relationship, so did subgroup III and subgroup IV. CaHDZ genes expressed specifically in different tissues and coordinately regulated the growth and development of pepper.

Key words: Capsicum annuum, HD-Zip gene family, systematic evolution, gene expression analyses