PENG Shi-qiao,LU Meng-dan,YANG Meng-qi,et al.Bioinformatic Analysis of PPR Gene Family in Soybean[J].Soybean Science,2021,40(02):177-185.[doi:10.11861/j.issn.1000-9841.2021.02.0177]
大豆PPR基因家族生物信息学分析
- Title:
- Bioinformatic Analysis of PPR Gene Family in Soybean
- Keywords:
- Soybean; PPR gene family; Bioinformatic analysis; Evolution; Phylogenetic analysis; Tissue specificity expression
- 文献标志码:
- A
- 摘要:
- 为明确大豆PPR基因家族在染色体上的分布、保守结构域、亚族种类、进化关系及表达特征等，采用生物信息学方法，基于Pfam的PPR种子序列模型筛选大豆基因组数据库，获得631个大豆PPR家族基因；利用MEME、ExPASy、TBtools、FigTree等工具对大豆PPR家族基因进行分类，分析各亚族的进化关系和保守结构域差异；筛选各亚族的代表基因，并进一步分析各亚族基因的保守率、等电点、UTR、CDS及基因表达特异性。结果表明：大豆PPR基因家族分为DYW、P、PLS、E/E+亚族以及1个未知亚族，其中DYW亚族为第一大亚族，占总基因数目的57.2%；各亚族基因在染色体上的分布是不均匀的，其内含子数目差异也较大，DYW亚族基因的内含子数目较少，但DYW亚族结构域种类最多，具有在C端出现特有的Motif7和Motif4的显著特征；但大豆PPR家族的各亚族基因表达特异性比较相似，均表现为叶片中高表达，花、根和茎中低表达；而且各亚族中都有大量成员缺失UTR；Glyma.19G095500、Glyma.11G086900、Glyma.02G175900和Glyma.01G158100 这4个基因具有独特的Motif8保守结构域，为新的亚族。
- Abstract:
- In order to find out soybean PPR genes and figure out the chromosomal distribution, the conserved domains, the subgrouping, the phylogenetic relationship and the expression characteristics of these genes, this study found 631 PPR genes through screening the soybean reference genome with the PPR model in the Pfam database. Clustering analysis was further performed to divide them into different subfamily with the softwares of MEME, ExPASy, TBtools and FigTree. The phylogenetic relationship and conserved domains of these subfamilies were also analyzed. We selected the representative genes from these subfamilies, and further evaluated their isoelectric points, UTR, CDS, and gene expression patterns. The results showed that, soybean PPR gene family could be divided into five subfamilies, DYW-, P-, PLS-, E/E+ and an unknown subfamily. Of them, DYW-subfamily was the biggest one, accounting for 57.2% of total soybean PPR genes. These subfamilies distributed unevenly in chromosomes, and their intron numbers varied greatly. DYW-subfamily contained fewer introns but contained more conserved motifs with two characteristical motifs of Motif7 and Motif4 locating in the C terminal. The representative genes of these subfamilies had a similar expression pattern with a high expression level in leaf but a low expression level in flower, root and stem. The UTR was missing in some members of these subfamilies. Glyma.19G095500, Glyma.11G086900, Glyma.02G175900 and Glyma.01G158100 were subgrouped into a new subgroup containing a unique motif of Motif8.
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备注/Memo
收稿日期：2020-10-27