水母雪兔子GPAT家族全基因组鉴定及表达分析

Genome-wide identification and expression analysis of the GPAT gene family in Saussurea medusa

关键词:  水母雪兔子,甘油-3-磷酸酰基转移酶,基因家族,生物信息学分析,组织特异性表达

Key words:  Saussurea medusa, glycerol-3-phosphate acyltransferase(GPAT), gene family, bioinformatics analysis, tissue-specific expression

摘要:

甘油-3-磷酸酰基转移酶(GPAT)在植物生长发育和适应逆境胁迫过程中具有重要作用,为探究GPAT基因家族成员对高山植物水母雪兔子(Saussurea medusa)适应高山极端生境时发挥的作用,该研究采用HMM和BLASTp方法对SmGPAT基因家族成员进行全基因组鉴定,对家族成员的理化性质、染色体定位、基因结构、保守基序和顺式作用元件进行分析,并基于转录组数据和qRT-PCR技术分析SmGPAT家族成员的组织表达模式。结果表明:(1)共鉴定出15个SmGPAT家族成员,随机分布在10条染色体上,分别编码357～566个氨基酸,蛋白质相对分子质量为40.16～63.86 kD,等电点为5.93～10.02,脂溶性指数为79.56～104.60,亚细胞定位预测位于线粒体或内质网(除SmGPAT7以外)。(2)系统进化分析发现,SmGPAT家族分为3个亚族(Group 1-Group 3),各亚族的基因结构和保守基序相似。SmGPAT家族蛋白质二级结构以α-螺旋和无规则卷曲为主,各亚族蛋白质三级结构模型相似。(3)顺式作用元件预测分析结果显示,SmGPAT家族含有大量逆境胁迫响应、激素响应和光响应相关的元件。(4)不同组织转录组数据分析结果表明,SmGPAT家族成员在叶和花中的表达量较茎和根高,并且qRT-PCR结果与转录组结果基本一致。综上认为,水母雪兔子中鉴定出的15个SmGPAT家族成员在不同组织间的表达模式存在差异,其中在花和叶中表达量较高,推测其在水母雪兔子叶和花发育过程中发挥重要作用,该研究为进一步开展SmGPAT基因在适应高山极端环境过程中的功能研究提供理论基础。

Abstract:

Glycerol-3-phosphate acyltransferase(GPAT)plays essential roles in plant growth and development and stress adaptation. To investigate the role of SmGPAT gene family members in Saussurea medusa's adaptation to alpine extremes, we performed genome-wide identification using HMM and BLASTp methods and analyzed physicochemical properties, chromosome localization, gene structures, conserved motifs, and cis-acting elements. We also examined expression patterns across tissues using transcriptomic data and qRT-PCR validation. The results were as follows:(1)A total of 15 SmGPAT family members were identified which randomly distributed on 10 chromosomes. These genes encoded 357-566 amino acid proteins(relative molecular mass of 40.16-63.86 kD)with isoelectric points of 5.93-10.02. Their aliphatic index ranged from 79.56 to 104.60. Subcellular localization predictions indicated that the SmGPAT gene was predominantly localized to mitochondria or the endoplasmic reticulum(except for SmGPAT7).(2)Phylogenetic analysis divided SmGPATs into three subgroups(Group 1 - Group 3), with members within subgroups shared similar gene structures and conserved motifs. The secondary structure of SmGPAT family protein mainly contained α-helix and random coil, and the tertiary structure models were similar across subgroups.(3)The prediction analysis of cis-acting elements revealed abundant stress-responsive, hormones-responsive, and light-responsive elements of SmGPAT family.(4)Transcriptomic data analysis showed higher SmGPATs expression levels in leaf and flower than in stem and root. qRT-PCR results were largely consistent with the transcriptomic results. In conclusion, the expression patterns of the 15 SmGPAT family members indentified in S. medusa vary among different tissues, with higher expression levels in flower and leaf. These findings suggest that SmGPAT members may play key roles in leaf and flower development in S. medusa. This study provides a theoretical basis for further functional investigations of SmGPAT genes adapting to the alpine extreme environment.