2024年3月29日 星期五
薄壳山核桃SnRK2基因家族鉴定及表达分析
Identification and expression analysis of SnRK2 gene family from Carya illinoinensis
2023年 第32卷 第2期 页码[18-28]    下载全文[16.6MB]  
摘要

 通过生物信息学方法从薄壳山核桃〔Carya illinoinensis (Wangenh.) K. Koch〕全基因组中鉴定出SnRK2基因家族成员,并对该基因家族成员编码蛋白的理化性质及基因的结构、保守基序、共线性关系、顺式作用元件和表达模式进行了分析。结果表明:从薄壳山核桃全基因组中鉴定出13个SnRK2基因,命名为CiSnRK2.1至CiSnRK2.13,编码氨基酸残基数为336~366,理论等电点均小于pI 7,且所有编码蛋白为亲水蛋白。13个CiSnRK2与10个拟南芥〔Arabidopsis thaliana (Linn.) Heynh.〕SnRK2的氨基酸序列高度保守,包含相同的结构域,如脱落酸(ABA)诱导调节结构域。13个CiSnRK2分为3组,薄壳山核桃与山核桃(C. cathayensis Sarg.)的SnRK2亲缘关系较近;每组中的CiSnRK2具有相似的保守基序和基因结构。13个CiSnRK2基因存在12对共线关系,Ka/Ks分析结果表明CiSnRK2基因进化过程主要受到正选择。CiSnRK2基因的启动子包含丰富的环境胁迫类及激素类响应元件,其中激素类响应元件以ABA响应元件最多。多数CiSnRK2基因在薄壳山核桃不同组织中有不同程度表达,其中CiSnRK2.5、CiSnRK2.8、CiSnRK2.9和CiSnRK2.12的表达水平较低,CiSnRK2.2、CiSnRK2.3和CiSnRK2.13的表达水平较高。经100 μmol·L-1 ABA处理24 h后,除CiSnRK2.2、CiSnRK2.3、CiSnRK2.6外,其余10个基因表达水平均上调。综合分析表明:薄壳山核桃SnRK2基因家族成员具有SnRK2基因家族的基本特征;该基因家族成员在不同组织中的表达特性存在差异,部分CiSnRK2基因的表达呈现组织特异性;ABA处理后部分CiSnRK2基因的表达水平显著上调,由此推断这些基因可能参与薄壳山核桃的ABA诱导响应过程。

Abstract

The SnRK2 gene family members were identified from the whole genome of Carya illinoinensis (Wangenh.) K. Koch by using bioinformatics methods, and the physicochemical properties of coding proteins of the gene family members, and their structures, conserved motifs, collinear relationships, cisacting elements and expression patterns were analyzed. The results show that 13 SnRK2 genes are identified from the whole genome of C. illinoinensis and named CiSnRK2.1 to CiSnRK2.13, the numbers of coding amino acid residues are 336-366, their theoretical isoelectric points are all smaller than pI 7, and all coding proteins are hydrophilic proteins. The amino acid sequences of 13 CiSnRK2s and 10 SnRK2s from Arabidopsis thaliana (Linn.) Heynh. are highly conserved, which contain the same domains such as abscisic acid(ABA)-inducible regulatory domain. Thirteen CiSnRK2s are divided into 3 groups, and the genetic relationships of SnRK2s between C. illinoinensis and C. cathayensis Sarg. are relatively close; CiSnRK2s in each group have similar conserved motifs and gene structures. There are 12 pairs of collinear relationships among 13 CiSnRK2 genes, and the Ka/Ks analysis result shows that the evolution of CiSnRK2 genes is mainly affected by positive selection. The promoters of CiSnRK2 genes contain abundant environmental stress and hormone response elements, and the ABA response elements are the most in hormone response elements. Most CiSnRK2 genes are expressed at different levels in different tissues of C. illinoinensis, in which, the expression levels of CiSnRK2.5, CiSnRK2.8, CiSnRK2.9 and CiSnRK2.12 are relatively low, while those of CiSnRK2.2, CiSnRK2.3 and CiSnRK2.13 are relatively high. After 100 μmol·L-1 ABA treatment for 24 h, except for CiSnRK2.2, CiSnRK2.3 and CiSnRK2.6, the expression levels of the other 10 genes are up-regulated. The comprehensive analysis shows that the SnRK2 gene family members from C. illinoinensis have the basic characteristics of SnRK2 gene family; there are differences in expression characteristics of these genes in different tissues, and the expressions of some CiSnRK2 genes show tissue specificity; the expression levels of CiSnRK2 genes are significantly up-regulated after ABA treatment, therefore, it is concluded that these genes may be involved in the response process of C. illinoinensis under ABA induction.

关键词薄壳山核桃; SnRK2基因; 生物信息学分析; 组织特异性表达; ABA诱导
Key wordsCarya illinoinensis (Wangenh.) K. Koch; SnRK2 gene; bioinformatics analysis; tissue specific expression; ABA induction
作者马文娟a,b,①, 朱凯凯a,b,①, 谌梦云a,b, 赵娟a,b, 谭鹏鹏a,b, 彭方仁a,b
所在单位南京林业大学: a. 南方现代林业协同创新中心, b. 林学院, 江苏 南京 21003
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基金项目中央财政林业科技推广示范项目(苏[2022]TG04); 江苏省自然科学基金项目(BK20190749)