SHI Li-song,ZHAO Xuan,FU Ya-li,et al.Bioinformatics and Tissue Expression Analysis of GAPDH Gene Family Under Abiotic Stress in Soybean[J].Soybean Science,2021,40(03):299-308.[doi:10.11861/j.issn.1000-9841.2021.03.0299]
大豆GAPDH家族基因生物信息学及其逆境组织表达分析
- Title:
- Bioinformatics and Tissue Expression Analysis of GAPDH Gene Family Under Abiotic Stress in Soybean
- Keywords:
- Soybean; Glyceraldehyde-3-phosphate dehydrogenase; Glycolysis; Bioinformatics; Abiotic stress; Amount of expression
- 文献标志码:
- A
- 摘要:
- 为探究大豆GAPDH家族基因应答非生物胁迫的机制，本研究采用同源分析、保守结构分析等方法对大豆GAPDH基因家族进行全基因组搜索，并对筛选出基因的系统发育关系、基因结构和保守基序、染色体分布、启动子区域的顺式作用元件进行分析，并研究了大豆GAPDH家族基因在不同组织中和非生物胁迫诱导后的表达模式。结果显示：在全基因组水平共搜索出19个大豆GAPDH家族成员，不均匀地分布在10条染色体上；亚细胞定位预测表明16个大豆GAPDH家族成员分布在叶绿体、细胞质和线粒体中；系统发育进化树将其分为4个亚家族SubⅠ、SubⅡ、Sub Ⅲ、Sub Ⅳ，且各个亚家族内基因的结构及保守基序具有高度保守性；基因启动子区域存在不同的与非生物胁迫响应和激素反应相关的顺式作用元件，推测其可能参与大豆非生物胁迫应答过程；大部分GAPDH基因在大豆不同组织中都有表达，并表现出明显的组织特异性；转录组分析发现分别有5和9个大豆GAPDH家族基因在干旱胁迫、盐胁迫下显著上调或者下调，其中GmGAPDH8和GmGAPDH9在干旱胁迫和盐胁迫下均显著上调表达。本研究对大豆GAPDH家族基因进行了系统分析，为进一步研究大豆的GAPDH家族基因在非生物胁迫应答过程中的调控作用提供理论基础。
- Abstract:
- In order to explore the response mechanism of soybean GAPDH family genes under abiotic stress, we searched the whole genome of soybean GAPDH gene family by homology analysis and conservative structure analysis, and analyzed the phylogenetic relationship, gene structure and conservative motif, chromosome distribution and cis-acting elements of promoter region. We studied the expression patterns of soybean GAPDH family genes in different tissues and after abiotic stress induction. The results showed that 16 GAPDH family members were unevenly distributed on 10 chromosomes at the whole genome level. The subcellular localization prediction revealed that the 16 GAPDH genes of soybean distributed on chloroplasts, cytoplasm and mitochondria. The phylogenetic analysis showed that these GAPDH genes could be divided into four subfamilies (SubⅠ, SubⅡ, Sub Ⅲ and Sub Ⅳ). Moreover, the gene structure and conserved motifs of each subfamily were highly conserved. Analysis of tissue expression patterns found that most GAPDH genes were expressed in different tissues, and showed obvious tissue specificity. Predictive analysis of promoter cis-acting elements found different homeopathic elements related to abiotic stress response and hormone response, which suggested that it may be involved in the abiotic stress response of soybean. In addition, transcriptome analysis found that, five and nine GAPDH family genes of soybean were significantly up-regulated or down-regulated respectively under drought stress and salt stress, GmGAPDH8 and GmGAPDH9 were significantly up-regulated under drought stress and salt stress. The systematic analysis of soybean GAPDH family genes provide a reference for further study of the regulatory role of soybean GAPDH family genes in abiotic stress response.
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备注/Memo
收稿日期：2020-12-23