甘蔗ScNRAMP基因家族的鉴定与生物信息学分析

Identification and bioinformatics analysis of ScNRAMP gene family in sugarcane

关键词:  甘蔗, 割手密, ScNRAMP, 基因家族, 重金属胁迫

Key words:  sugarcane, Saccharum spontaneum, ScNRAMP, gene family, heavy metal stress

摘要:

NRAMP蛋白(natural resistance-associated macrophage proteins)家族在植物响应重金属胁迫时具有重要作用,能够转运Fe²⁺、Mn²⁺、Zn²⁺和Cd²⁺等重金属离子。为探究甘蔗ScNRAMP基因家族的特征,该文基于甘蔗割手密基因组鉴定了ScNRAMP基因家族,并进行了理化特性、基因结构、顺式作用元件、保守基序、结构域和进化关系等分析。结果表明:甘蔗ScNRAMP基因家族含有29个成员,不均匀分布在19条染色体上; 编码蛋白均为不稳定蛋白,无信号肽,亚细胞均定位在质膜上; 各成员保守基序有6～10个不等,跨膜数有6～12个不等,二级结构主要构成元件为α-螺旋和无规则卷曲; 顺式作用元件分析表明甘蔗ScNRAMP基因家族可能通过激素代谢参与逆境胁迫和生长发育等生物过程; 利用割手密的RNA-seq转录组表达数据进行的组织特异性分析发现,ScNRAMP在甘蔗不同发育阶段的叶和茎中具有时空表达特性; 进化树分析将甘蔗ScNRAMP家族成员分为3个亚家族(I、Ⅱ和Ⅲ)。该研究在全基因组水平上系统地鉴定了现代栽培甘蔗祖先种之一割手密NRAMP基因家族,既为进一步了解甘蔗NRAMP基因家族提供了基础,也为后续甘蔗重金属研究提供了重要候选基因。

Abstract:

NRAMP(natural resistance-associated macrophage proteins), which can transport metal ions such as Fe²⁺, Mn²⁺, Zn²⁺ and Cd²⁺, plays an essential role in response to heavy metal stress in plant. To better understand the characteristics of the ScNRAMP gene family, bioinformatics methods were employed to identify and comprehensively analyze ScNRAMP gene family which includes protein physicochemical properties, gene structure, cis-acting elements, conserved motif, domain and evolutionary relationships. The results were as follows: A total of 29 ScNRAMP genes were identified in the Saccharum spontaneum genome; These 29 genes were unevenly distributed on 19 chromosomes, and contained 6 to 10 conserved motifs; The encoded proteins were all unstable proteins with no signal peptides and the subcellular locations were all on the plasma membrane; The number of membranes ranged from 6 to 12, and the secondary structure was composed of α-helix and random coils as the main components; Moreover, cis-acting elements analysis suggested that ScNRAMP may be involved in regulation of stress and development by involving in phytohormone metabolism; The tissue-specific analysis based on RNA-seq transcriptomics expression data of Saccharum spontaneum, showed that spatiotemporal expression of 29 ScNRAMP genes in the leaves and stems of sugarcane at different development stages; Phylogenetic analysis showed that the 29 ScNRAMP genes can be divided into three subfamilies(I, Ⅱ and Ⅲ). This study can be useful to better understand the ScNRAMP gene family and provide significant candidate genes that respond to the stress of heavy metals in sugarcane for further study.