基于全基因组的三七HMA基因家族鉴定与生物信息学分析

Identification and Bioinformatics Analysis of HMA Gene Family Based on Panax notoginseng Genome

三七[Panax notoginseng (Burk.) F.H.Chen]作为中国重要的药用植物,具有较强的金属元素吸收富集特性,重金属ATP酶(heavy metal transporting ATPase,HMA)家族已被证明参与了众多二价金属离子的吸收转运,然而目前在三七中还没有关于金属元素吸收转运相关研究。本研究从三七全基因组中鉴定了10个HMAs基因家族成员(PnHMAs),PnHMA1~PnHMA3属于铜(Cu)/银(Ag)亚组,PnHMA4~PnHMA10属于锌(Zn)/钴(Co)/镉(Cd)/铅(Pb)亚组;PnHMAs均被预测定位于质膜或叶绿体上,PnHMA10与其他成员间蛋白理化性质差异较大;不同亚组成员间基因结构、蛋白结构域和保守基序模式与系统发育的多样性密切相关,它们均具有不同的金属离子转运相关功能,但具体转运的离子存在差异;片段复制和串联重复可能是PnHMAs家族基因在三七基因组中扩增和进化的主要原因之一;组织表达特异性表明,PnHMA6和PnHMA10在芦头中高表达,PnHMA7在主根中高表达,PnHMA3和PnHMA5在茎中高表达,PnHMA1、PnHMA2和PnHMA9在叶中高表达,PnHMA3、PnHMA4和PnHMA8在花中高表达;Cd胁迫下,PnHMAs在三七根部上调表达。密码子偏好性和异源表达适配受体分析发现,PnHMAs基因家族偏好使用以A/T结尾的密码子,且自然选择是其密码子偏好性的主要影响因素,酿酒酵母可作为其异源表达适配受体。本研究为今后三七金属元素候选基因的筛选和功能研究提供了前期生物信息学基础。

As a valuable medicative plant in China,Panax notoginseng(Burk.) F.H.Chen contains a robust character of metal uptake and deposition,and the heavy metal transporting ATPase(HMA) family takes to participate within the uptake and transport of the many bivalent metal ions.However,there are not any studies on metal part absorption and transport in P.notoginseng.During this study,10 HMAs members of the family(PnHMAs) were identified from the whole genome of P.notoginseng,among them,PnHMA1~PnHMA3 belonged to the copper(Cu)/silver(Ag) subgroup and PnHMA4~PnHMA10 belonged to the zinc(Zn)/cobalt(Co)/cadmium(Cd)/lead(Pb) subgroup.All Pn HMAs predicted to be localized at the plasma membrane or chloroplast;PnHMA10considerably differed from other members in their physicochemical properties;genetic structure,conserved domain,and conserved motif patterns were closely associated with phylogenetic diversity among members of various subgroups,all with different metal ion transport-related functions,but the precise ions transported differed;the segment and tandem duplication could also be one in all the most reasons for the amplification and evolution of PnHMAs family genes within the P.notoginseng genome;tissue expression specificity indicated that PnHMA6 and PnHMA10 were highly expressed within the rhizomes,PnHMA7 was highly expressed in roots,PnHMA3 and PnHMA5 were highly expressed within the stems,PnHMA1,PnHMA2 and PnHMA9 were highly expressed in leaves,and PnHMA3,PnHMA4 and PnHMA8 were highly expressed in flowers;Cd upregulates the expression of PnHMAs in P.notoginseng roots.The analysis of codon usage bias and adaptive receptor for heterologous expression discovered that the PnHMAs family most popular to use codons ending with A/T,additionally,natural selection was the main factor that caused their codon usage bias,and saccharomyces cerevisiae could be used as an adaptive receptor for heterologous expression.This study provides a bioinformatic foundation on the screening of candidate genes associated with metal transport and also the studies on gene function identification in P.notoginseng.