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三浅裂野牵牛ItfGAD基因家族全基因组鉴定与表达分析

Genome-wide identification and expression analysis of the ItfGAD gene family in Ipomoea trifida (Kunth) G. Don

  • 摘要: 三浅裂野牵牛(Ipomoea trifida (Kunth) G. Don)为二倍体,是甘薯(Ipomoea batatas (L.) Lam.)的野生近缘种,其基因组结构简单,便于基因定位和功能研究,可为解析甘薯复杂的六倍体基因信息及功能提供参考。谷氨酸脱羧酶(Glutamate decarboxylase,GAD)作为γ-氨基丁酸(γ-aminobutyric acid,GABA)支路合成途径的关键酶基因,对GABA的合成有着重要的作用。本研究利用生物信息学方法在三浅裂野牵牛全基因组中共鉴定获得15个ItfGADs基因家族成员,根据其在染色体上的顺序分别命名为ItfGAD1~ItfGAD15。结果显示,ItfGADs蛋白大多数为酸性蛋白,各成员的氨基酸序列长度为476~537 aa,等电点为5.69~8.7。ItfGADs蛋白的二级结构分析结果表明,它们均以α-螺旋和无规则卷曲为主。亚细胞定位预测结果发现,11个ItfGAD蛋白定位于细胞质中。ItfGADs蛋白均含有一个相对保守的PLP氨基酸结合位点。系统进化分析结果表明,15个ItfGADs家族成员可分为4个进化分支,不同ItfGADs成员之间保守基序、外显子和内含子数目及分布差异较大。转录组表达谱数据和qRT-PCR实验结果均显示,ItfGADs基因家族成员在三浅裂野牵牛不同组织和不同胁迫处理下具有表达特异性。其中,ItfGAD4在茎中的表达量最高;ItfGAD5ItfGAD14在根中的表达量相对较高;ItfGAD6、ItfGAD9ItfGAD12在叶中的表达量最高。在盐、干旱胁迫下,各基因在根与叶组织中响应时间、表达峰值、变化趋势各不相同,推测它们可能参与三浅裂野牵牛的胁迫响应并在特定组织发挥重要作用。

     

    Abstract: Sweet potato (Ipomoea batatas (L.) Lam.) is a major global food crop with a complex hexaploid genome, whereas its wild diploid relative I. trifida (Kunth) G. Don possesses a simpler genomic architecture that serves as a valuable reference for elucidating gene function and structural evolution in I. batatas. Glutamate decarboxylase (GAD), a key enzyme in the γ-aminobutyric acid (GABA) branch biosynthesis pathway, catalyzes the conversion of glutamate to GABA and plays a crucial role in plant stress responses. In this study, 15 ItfGAD genes were identified in the I. trifida genome, designated ItfGAD1 to ItfGAD15 based on their chromosomal location. Bioinformatic analyses revealed that most ItfGAD proteins were acidic, with amino acid (aa) lengths ranging from 476 to 537 and isoelectric points (pI) between 5.69 and 8.7. Secondary structure prediction indicated that α-helices and random coils predominated. Subcellular localization analysis suggested that 11 ItfGAD proteins were cytoplasmic. Multiple sequence alignment showed that all ItfGAD proteins contained a highly conserved PLP-binding domain, and phylogenetic analysis classified them into four distinct evolutionary branches. The number and distribution of conserved motifs, exons, and introns varied considerably among different ItfGADs, suggesting functional diversification. Transcriptomic and qRT-PCR analyses demonstrated tissue-specific and stress-responsive expression patterns. ItfGAD4 exhibited the highest expression in stems, ItfGAD5 and ItfGAD14 were predominantly expressed in roots, and ItfGAD6, ItfGAD9, and ItfGAD12 exhibited maximal expression in leaves. Under salt and drought stress, response times, expression peaks, and variation trends differed among genes in root and leaf tissues, indicating distinct regulatory roles in abiotic stress adaptation. Collectively, these results provide a comprehensive framework for understanding the biological and regulatory functions of the ItfGAD gene family and offer novel insights into the molecular mechanisms that mediate responses to abiotic stress tolerance in I. trifida.

     

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