苹果Hsf家族成员的序列特征、表达与进化分析

Sequence Characterization,Expression,and Evolutionary Analysis of Heat Shock Transcription Factors in Apple

为全面了解苹果基因组中热激转录因子(Hsf)的序列特征及进化,采用生物信息学手段,在苹果全基因组水平上鉴定出50个MdHsf基因,并对其系统发育关系、序列特征、表达情况以及选择压力进行详细分析。系统发育与序列分析显示:与拟南芥和水稻相似,50个MdHsf基因可分为A、B、C 3个亚族;2个或多个MdHsf基因位于同一个末端进化支,说明该基因家族在苹果中发生了物种特异性扩增;尽管MdHsf基因的内含子数目和长度变异较大,但其蛋白的保守基序和功能结构域具有较高的保守性,这可能与功能约束有关。基于EST数目,可推知:除了MdHsfA2a和MdHsfA3a/b/c等14个基因没有相应的EST外,其余72%的基因都有转录活性。选择压力检测和结构建模分析显示:在36个MdHsf蛋白的选择压力检测中,位点模型未鉴定到正选择位点的存在;而在显著水平下(P<0.05),分支-位点模型在d和e进化分支上,共检测到5个正选择位点,它们是28R、30L、35D、51M、67V,其中28R和30L位于Hsf结构域中,35D、51M和67V位于Hsf结构域之外,这说明除了MdHsfA4d/e和MdHsf C1a/b发生快速进化外,其他成员受控于纯净选择,具有高度保守性。综合以上研究结果,苹果基因组中存在多种热激转录因子,其蛋白的保守基序和功能结构域具有较高保守性,大多具有转录活性,在进化上该家族受纯净选择主导。

To extensively understand the sequence feature and evolution of heat shock transcription factors（Hsf）in the genome of apple,fifty MdHsf genes were identified using bioinformatics methods at the whole-genome level of apple,and a series of analysis including sequence characterization,phylogenetic relationship,gene expression and selective pressure of MdHsf genes were further performed.Phylogenetic relationship and sequence characterization analysis showed that,like the model species Arabidopsis and rice,50 MdHsf genes were divided into three subfamilies A,B and C.Additionally,at least two genes were found in the same end clades in the phylogenetic tree,indicating that the lineage-specific amplification had happened during evolutionary processes of apple Hsf gene family.Although the intron numbers and sizes of MdHsf genes were relatively divergent,the conserved motifs and domains of MdHsf proteins were highly conserved because of functional constraints.Based on EST data,72% of the 50 genes（except 14 genes such as MdHsfA2a and MdHsfA3a/b/c）had transcription activities.Selective pressure signatures demonstrated that no positive selection site was identified in the cleaned codon alignments for 36 MdHsf genes based on site-specific model,suggesting that this protein family was controlled by purifying selection.However,branch-site model had identified a total of five positively selected sites in the d and e clade of the phylogenetic tree,i.e.28R,30L,35D,51M and 67V.28R and 30L were included in the Hsf domains,while 35D,51M and 67V were not mapped on the region of Hsf domains,suggesting that purifying selection was the main evolutionary dynamics of functional conservation Hsf domains except for 28R and 30L.In conclusion,various Hsfs existed in apple genome,and the conserved motifs and functional domains were conserved.The majority of them had transcription activity,and the evolution of this family was dominated by purifying selection.