Abstract
Background: Histones are major components of chromatin, which is a nucleosome structure associated with chromosome segregation, DNA packaging and transcriptional regulation. Histone H3 is encoded by many genes in most eukaryotic species, but little information is known about the Histone H3 gene family in cotton.Results: In this study, we identified and analyzed the evolution and expression of histone H3 gene family in cotton. First, 34 G. hirsutum genes were identified belonging to the H3 gene family which were divided into four subclasses: CENH3, H3.1, H3.3 and H3-like. Among these H3.1 subclass contained the highest number of genes (22 members) followed by H3.3 subclass (9 members). In addition, there were18 and 16 H3 genes identified in G. arboretum and G. raimondii, respectively. Furthermore, we conducted conserved sequence analysis of H3 proteins, and found that the four amino acids signature including A31F41S87A90 for H3.1 and T31Y41H87L90 for H3.3 could be used to discriminate H3.1 from H3.3. The expression of H3 gene family varied in different tissues and developmental stages of G. hirsutum, where H3.1 subclass genes play a critical role in pistil development. By virus-induced gene silencing of GhCENH3 (Gh_D07G1382) gene, the size of leaf got smaller with pYL156-CENH3 than that with pYL156 in TM-1. Whereas, the number of the stomata in the leaf epidermis and number of chloroplasts in the leaf stomatal guard cells by pYL156-CENH3 was more than that by pYL156 and pYL156-PDS.Conclusions: Four sub-classes (CENH3, H3.1, H3.3 and H3-like) of H3 gene family were highly conserved in cotton during the rapid phase of evolution among which CENH3 is necessary for leaf growth. These findings are useful for providing further insights into cotton biology and breeding.