江西铅山红芽芋叶绿体基因组特征及系统发育分析

Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan

为分析江西铅山红芽芋叶绿体基因组的结构组成情况,判定其在芋属中的进化位置及与同芋属叶绿体基因组的区别,为芋属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina NovaSeq 6000测序平台对江西铅山红芽芋叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,并利用Geneious、MISA、MAFF、FASTTREE、CUSP、Chips和Codon W等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、SSR位点和系统发育进行分析。结果表明,江西铅山红芽芋叶绿体基因组大小为16 2544 bp,呈现四分体结构。共包含130个基因,其中84个编码蛋白质的基因,37个t RNA基因,8个核糖体rRNA基因,1个假基因。通过密码子偏好性分析,平均有效密码子数为45.60,ENC值小于45的基因39个,说明其密码子偏好性强。通过SSR分析,检测到101个SSR位点,其中单核苷酸重复最多(约占83.17%),且单核苷酸以A/T型为主。与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高。此外,系统发育分析发现江西铅山红芽芋与芋属、岩芋属聚为一支。本研究得到了江西铅山红芽芋的叶绿体基因组基本情况与系统发育位置,为江西铅山红芽芋的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。

In order to analyze the structure and composition of the chloroplast genome of Colocasia esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan,its evolutionary position in Colocasia genus and its difference from the chloroplast genome of the same genus were determined,which may provide relevant basis for species identification,genetic diversity analysis and resource protection of Colocasia genus.The Illumina NovaSeq 6000 sequencing platform was used to sequence the genome of the chloroplast of C.esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan.Bioinformatics analysis methods were to conduct sequence assembly,annotation and feature analysis,and bioinformatics software such as Geneious,MISA,MAFF,FASTREE,CUSP,Chips and Codon W were used to analyze the genome structure and number,codon preference,sequence duplication,SSR sites and phylogeny.The results showed that the chloroplast genome size of C.esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan was 162544 bp,showing a tetrad structure.It contained 130 genes,including 84 protein coding genes,37 tRNA genes,8 ribosomal rRNA genes and 1 pseudogene.By codon preference analysis,the average number of effective codons was 45.60,and 39 genes with ENC value<45,indicating strong codon preference.Through SSR analysis,101 SSR sites were detected,of which single nucleotide repeats were the most(about 83.17%),and single nucleotide was mainly A/T type.Compared with related species,the chloroplast genome sequence was highly conserved,especially the protein coding sequence was highly similar.In addition,the phylogenetic analysis showed that C.esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan was clustered into one branch with Colocasia genus and Remusatia genus.This study obtained the basic information of chloroplast genome and phylogenetic location of C.esculenta L.Schoot var.cormosus cv.‘Hongyayu’from Jiangxi Yanshan,and provided a preliminary study for its species identification,genetic diversity of natural population and functional genomics.