基于Illumina高通量测序技术的草豆蔻基因组研究  

Genome survey study of Alpinia katsumadai based on Illumina high throughput sequencing

作　　者：郑燕 何志凯 姚梦鹃 郭云端 陈曦荣 涂梦薇 张勇洪 李琛 ZHENG Yan;HE Zhi-kai;YAO Meng-juan;GUO Yun-duan;CHEN Xi-rong;TU Meng-wei;ZHANG Yong-hong;LI Chen(Laboratory of Medicinal Plant,Institute of Basic Medical Sciences,Hubei University of Medicine,Shiyan 442000,China;The First Clinical College,Hubei University of Medicine,Shiyan 442000,China;Hubei Key Laboratory of Wudang Local Chinese Medicine Research,Biomedical Research Institute,Hubei University of Medicine,Shiyan 442000,China)

机构地区：[1]湖北医药学院基础医学院药用植物实验室,湖北十堰442000 [2]湖北医药学院第一临床学院,湖北十堰442000 [3]湖北医药学院生物医药研究院武当特色中药研究湖北省重点实验室,湖北十堰442000

出　　处：《中草药》2020年第13期3530-3534,共5页Chinese Traditional and Herbal Drugs

基　　金：国家自然科学基金资助项目(31701294);湖北医药学院高层次人才启金资助项目(2017QDJZR26);湖北省卫生健康委员会项目(ZY2019Q004);药用资源与天然药物化学教育部重点实验室开放基金资助项目(2019005);湖北重点实验室建设基金资助项目(WLSP201905)。

摘　　要：目的对药食同源植物草豆蔻Alpinia katsumadai进行基因组调研分析,完善草豆蔻基因组遗传信息。方法研究采用Illumina高通量测序技术,基于K-mer分析手段来研究草豆蔻基因组的大小及杂合度,利用MISA方法分析可能的SSR分子标记。结果草豆蔻的基因组大小为1.60 Gb,基因组杂合度为0.44%,重复序列比例为72.72%;在基因组序列中,进行SSR分子标记分析,共鉴定出了364 395个SSR,其中,单、双、三核苷酸重复模体的比例较高,分别占比64.25%、24.05%、10.31%;从测序得到的350 bp文库中,随机取10 000条单端reads,与NT库进行BLAST比对,发现草豆蔻的近缘物种艳山姜Alpinia zerumbet和小豆蔻Elettaria cardamomum上的reads数分别占比对上NT库reads数的12.89%和12.36%。结论通过对草豆蔻植物的基因组大小、杂合度调查及SSR分子标记分析表明,草豆蔻物种基因组属于高重复、大基因组的复杂基因组,这为草豆蔻的资源保护和遗传多样性分析及品种选育提供了遗传信息支撑。Objective To analyze the genome survey of medicinal and edible plant Alpinia katsumadai and complete its genome genetic information. Methods This study was based on high throughput sequencing platform Illumina, and K-mer analysis was applied to estimate the genome size and heterozygosity rate of A. katsumadai. Meanwhile, simple sequence repeat(SSR) loci that were suitable as markers were identified by MISA software. Results The estimated genome size of A. katsumadai was 1.60 Gb, with a 0.44% heterozygosity rate and 72.72% repeats;In the genome sequence, 364 395 simple sequence repeats(SSRs) were detected by SSR molecular marker analysis, among which mono-nucleotide, di-nucleotide and tri-nucleotide repetitive motifs ranked the higher percentages of 64.25%, 24.05% and 10.31%, summed up to 98.61%;From the 350 bp library obtained by sequencing, 10 000 single-end reads were randomly selected and blasted with NT bank, the results showed that its genetically close species Alpinia zerumbet and Elettaria cardamomum were blasted with the reads of 12.89% and 12.36% in NT bank. Conclusion The genome size, heterozygosity rate and SSR molecular marker analysis’ genome survey study on A. katsumadai indicated that the genome of A. katsumadai species was a complex, highly repetitive and large genome, which provided genetic information support for the resource protection, genetic diversity analysis and variety breeding of A. katsumadai.

关 键 词：高通量测序 草豆蔻 基因组大小 杂合度 简单重复序列 

分 类 号：R282.12[医药卫生—中药学]