甜菜组蛋白去乙酰化酶(HDACs)基因家族鉴定及功能预测

为了鉴定甜菜基因组中春化作用相关的组蛋白去乙酰化酶(HDACs)。本研究利用HMMsearch和Blastp鉴定BvHDACs基因家族成员,并采用iqtree程序构建最大似然进化树。利用TBtools分析BvHDACs染色体定位、基因结构。通过转录组测序分析春化过程中BvHDACs表达模式。结果表明,甜菜共有16个的BvHDACs基因分别位于5条染色体。它们可分为RPD3/HDA1、SIR2、HD2三个亚家族,亚家族内各成员功能结构域高度相似。转录组测序表明多个RPD3/HDA1、SIR2和HD2成员在春化过程中发生显著变化。尤其是,BvHDT1和BvHDT2变化趋势与抽薹表型变化具有相关性。蛋白互作预测表明BvHDT1、BvHDT2具有与BvFLD、BvJMJ11、BvJMJ12等抽薹开花相关蛋白相互作用的潜力。综上,推测BvHDT1和BvHDT2可能参与甜菜春化作用。

Histone Deacetylases (HDACs) Gene Family in Sugar Beet: Identification and Functional Prediction

To identify vernalization-related histone deacetylases (HDACs) in sugar beet genome, HMMsearch and Blastp were employed to identify the members of BvHDACs gene family, and iqtree program was used to construct the maximum-likelihood phylogenies. The chromosome location and gene structure of BvHDACs were analyzed by TBtools. The expression pattern of BvHDACs under vernalization was measured by RNA-seq. The results showed that there were 16 BvHDACs located on 5 chromosomes. BvHDACs were classified into 3 subfamilies, namely RPD3/HDA1, SIR2 and HD2, and members from the same subfamily had similar functional domain. According to RNA-seq, the expression of several genes from RPD3/HDA1, SIR2 and HD2 significantly changed after vernalization. Especially, the expression of BvHDT1 and BvHDT2 were correlated with changes of bolting-related phenotype. The protein-protein interaction prediction showed that BvHDT1 and BvHDT2 possibly interacted with BvFLD, BvJMJ11 and BvJMJ12, which were involved in flowering and bolting. In summary, it is hypothesized that BvHDT1 and BvHDT2 may be involved in vernalization of sugar beet.