摘要
为明确红芽芋、荔浦芋叶绿体基因组的基本特征及其差异,本研究以江西铅山红芽芋和广西荔浦芋为研究对象,采用改良CTAB法提取2种芋新鲜叶片基因组DNA,利用高通量测序技术获得2种芋全长叶绿体基因组序列,并进行SSR检测、序列比对、遗传多样性滑窗分析和系统发育树构建分析。结果表明,红芽芋和荔浦芋的叶绿体基因组全长分别为162478 bp和162453 bp,均呈现典型的环状双链四分体结构,二者均注释到131个基因,包括蛋白编码基因86个,tRNA基因37个,rRNA基因8个,其中具有2个拷贝的基因18个,具有内含子的基因23个。简单重复序列(SSR)位点分析发现,红芽芋和荔浦芋基因组序列分别含有130和124个SSR,二者SSR序列中A/T碱基含量分别占63.08%和61.29%,基于其SSR位点分析开发出15条具有多态性的SSR引物。红芽芋和荔浦芋叶绿体基因组共检测到236个SNP位点,26.7%的SNP位点发生在编码区,其中有25个基因发生错位突变,这些基因的变异可能促进了2种芋之间的性状变异。与天南星亚科已公布的13个属代表植物叶绿体基因组进行比较,其基因结构、种类和数量都比较保守,trnS-trnG和ndhF-rpl32分别是SSC区和LSC区的最高变异位点。最大似然法构建的系统发育树显示芋属与皂七属亲缘关系最为相近,与斑龙芋属亲缘关系较远。本研究结果将为我国特色芋种质资源开发利用、遗传多样性评价和系统发育分析奠定理论基础。
To confirm the characteristics and difference of the chloroplast(cp)genome of Colocasia esculenta var.Redbud and Colocasia esculenta var.Lipu,the two taros were taken as experimental materials in the study,their genomic DNA were first extracted form fresh leaves using an improved CTAB method and the two complete cp genomes were obtained using high-throughput sequencing technology and bioinformatics analysis,simple sequence repeat(SSR)identification,multiple sequence alignment,sliding window analysis on DNA polymorphism and phylogenetic tree analysis were then conducted on two complete cp genomes.The results showed that the length of the complete cp genomes of Redbud and Lipu was 162478 bp and 162453 bp,respectively,exhibiting the typical cyclic quadripartite structure.A total of 131 genes were annotated both in the two,including 86 protein-coding genes,37 tRNA genes and 8 rRNA genes,of which 18 genes had two copies and 23 genes had introns.A total of 130 and 124 SSR sites were identified in Redbud and Lipu respectively,the content of A/T in the SSR repeats was 63.08%and 61.29%respectively.15 SSR polymorphic primers were identified.A total of 236 cp single nucleotide polymorphism(SNP)sites were detected between Redbud and Lipu,of which 26.7%were in the gene coding region,which leading to 25 missense variant genes,the variation of the genes may promote the difference between the two varieties.Compared with the representative species from 13 genus of Aroideae showed that the structure,types,and numbers of gene were relatively conservative.The trnS-trnG and ndhF-rpl32 were the highest variation sites in SSC and LSC region,respectively.The phylogenetics analysis using maximum likelihood method(ML)showed that the genus Colocasia had the closest relationship with the genus Steudnera,but the farthest relationship with the genus Sauromatum in the Ariodeae.The results would provide a theoretical basis for the germplasm resource exploitation,genetic diversity evaluation and phylogenetic analysis of C.esculenta.
作者
贾芯碧
潘饶
肖遥
罗莎
单楠
孙静宇
汪生林
周庆红
黄英金
朱强龙
JIA Xinbi;PAN Rao;XIAO Yao;LUO Sha;SHAN Nan;SUN Jingyu;WANG Shenglin;ZHOU Qinghong;HUANG Yingjin;ZHU Qianglong(Jiangxi Province Key Laboratory of Root and Tuber Crops Biology/Jiangxi Agricultural University,Nanchang,Jiangxi 330045,China)
出处
《热带作物学报》
CSCD
北大核心
2023年第5期880-893,共14页
Chinese Journal of Tropical Crops
基金
国家自然科学基金项目(No.32060683)
江西省自然科学基金项目(No.20202ACBL215006)
江西重点研发计划项目(No.20212BBF61001)。
关键词
红芽芋
荔浦芋
叶绿体基因组
SSR
SNP
系统发育分析
Colocasia esculenta var.Redbud
Colocasia esculenta var.Lipu
chloroplast genome
SSR
SNP
phylogenetic analysis
