摘要
目的基于基因组调研分析,研究药用植物胶州延胡索的基因组遗传信息。方法采用Illumina高通量测序技术,借助K-mer分析工具揭示胶州延胡索的基因组大小、杂合率和鸟嘌呤-胞嘧啶(guanine-cytosine,GC)含量等分子遗传学特征,利用微卫星序列识别工具(microsatellite identification tool,MISA)分析其简单重复序列(simple sequence repeat,SSR)特征。结果结果表明胶州延胡索为三倍体,基因组的大小约为573.97 Mb,基因组的GC含量为39.18%;根据样品K-mer曲线偏离泊松分布,推测该样品的高杂合基因组杂合度为1.71%,重复序列比例为65.53%。提取reads中前50000条序列与核苷酸序列(nucleotide,NT)数据库进行基本局部比对搜索工具(basic local alignment search tool,BLAST)比对,结果显示,五台山延胡索Corydalis hsiaowutaishanensis T.P.Wang是比对上最多的物种,占比38.97%,表明胶州延胡索与同科同属植物五台山延胡索的来缘关系较近。此外对基因组序列进行SSR特征分析,共鉴定出864360个SSR,其中单核苷酸、二核苷酸、三核苷酸重复基序的占比依次为77.0%、11.6%、9.7%。结论胶州延胡索的复杂基因组高杂合、高重复,该研究为构建延胡索精细测序基因组文库提供依据,同时为其基因资源的保护、利用以及SSR分子标记的开发和应用提供参考。
Objective To develop genetic resources of the medicinal plant Corydalis kiautschouensis V.Poelln.based on genomic investigation and analysis.Methods In this study,Illumina high-throughput sequencing technology and K-mer analysis tools were employed to elucidate the molecular genetic characteristics of Corydalis kiautschouensis,including genome size,heterozygosity,guanine-cytosine(GC)content,and to develop simple sequence repeat(SSR)molecular markers using microsatellite identification tool(MISA)software.Results The assembly analysis revealed that Corydalis kiautschouensis is a triploid with an estimated genome size of 573.97 Mb and a GC content of 39.18%.The deviation of the sample’s K-mer curve from Poisson distribution suggested a highly heterozygous genome,exhibiting a heterozygosity rate of 1.71%and repetitive sequences accounting for 65.53%.The first 50000 reads were extracted and aligned against the nucleotide(NT)database using basic local alignment search tool(BLAST),demonstrating the highest sequence match rate(38.97%)with Corydalis hsiaowutaishanensis T.P.Wang,indicating a close phylogenetic relationship between Corydalis kiautschouensis and this congeneric species.Additionally,SSR molecular genetic markers were predicted and developed based on detected gene sequences,totaling 864360 markers,with single nucleotide,dinucleotide,and trinucleotide repeat motifs accounting for 77.0%,11.6%,and 9.7%,respectively.Conclusion The genome of Corydalis kiautschouensis V.Poelln.is characterized by a high proportion of repetitive sequences and is considered a complex genome with high heterozygosity.This study provides a reference for constructing a library for fine sequencing of the genome and offers a molecular basis for the development of SSR molecular markers,as well as for the protection and utilization of genetic resources.
作者
张娜
王坦
徐皓
杨洁
符纯美
牛恒磊
徐顶巧
ZHANG Na;WANG Tan;XU Hao;YANG Jie;FU Chunmei;NIU Henglei;XU Dingqiao(College of Pharmacy,Hanzhong Vocational and Technical College,Hanzhong 723002,China;No.1 Internal Medicine Department,Affiliated Hospital of Hanzhong Vocational and Technical College,Hanzhong 723000,China;College of Biological Science and Engineering,Shaanxi University of Technology,Hanzhong 723000,China;College of Pharmacy,Shaanxi University of Chinese Medicine,Xianyang 712046,China)
出处
《西北药学杂志》
2025年第4期16-21,共6页
Northwest Pharmaceutical Journal
基金
秦创原中医药产业创新聚集区项目(编号:L2024-QCY-ZYYJJQ-X69、L2024-QCY-ZYYJJQ-X38)
秦巴生物资源与生态环境国家重点实验室项目(编号:SXC-2019)
陕西中医药大学科技创新人才体系建设计划项目(编号:2023)
陕西省科技厅重点研发计划社发项目(编号:2022SF-543)
汉台区科学技术计划项目(编号:2021KX-07)。
关键词
胶州延胡索
基因组大小
杂合率
简单重复序列
Corydalis kiautschouensis V.Poelln
genome size
heterozygosity rate
simple sequence repeat
