基于基因组和转录组数据的胡椒内参基因鉴定

The Identification of Internal Control Genes Based on Genome and Transcriptome Data in Black Pepper(Piper nigrum L.)

为系统筛选适合胡椒基因表达模式分析的内参基因,本研究基于胡椒全基因组和转录组数据,初步筛选出62个候选基因。以胡椒主根、芽尖、叶片、花穗、不同发育时期果实以及接种辣椒疫霉菌的主蔓为材料,利用geNorm、NormFinder和BestKeeper软件系统分析候选基因在不同组织中的表达稳定性,结合目标基因的表达模式验证,鉴定稳定表达最优的内参基因为Myeloid leukemia factor 1(Pn17.1212)。结果表明:该基因是分析胡椒果实发育、辣椒疫霉菌响应相关基因表达模式的理想内参。内参基因的选择不应仅限于持家基因,全基因组和转录组信息可提供更加全面的参考基因数据,内参基因的准确鉴定需综合转录组信息、基因表达稳定性、标记基因的表达模式验证等数据分析的结果,获得的理想内参基因可满足不同研究对表达稳定性的要求。

In order to identify the internal control gene for the gene expression analysis in black pepper,62 candidate internal control genes were selected by a preliminary assessment of genome and transcriptome data.The stability of gene expression was investigated using geNorm,NormFinder and BestKeeper in a diverse set of 16 samples,including root,shoot apices,leaf,flower,fruits at different developmental stages and the stems at different time after inoculated with Phytophthora capsici.By combining with the expression pattern of target gene,the gene Myeloid leukemia factor 1(Pn17.1212)with ideal stable expression was identified.It can be considered as an ideal internal control gene in the analysis gene expression pattern of fruit development and Phytophthora capsica infection.The selection of internal reference genes should not be limited to housekeeping genes,the genome and transcriptome data could provide more candidate genes.The identification of internal reference genes should require a comprehensive analysis such as transcriptome,expression stability and expression pattern validation of marker genes.An ideal internal control gene could be applied in different researches with different requirement of the stability of expression.