基于流式细胞术和K-mer分析的荆芥基因组大小评估  

Genome-determination of Nepeta cataria Based on Flow Cytometry and K-mer Analysis

作　　者：姜涛 刘灵娣[1] 田伟[1] 刘铭[1] 温春秀[1] JIANG Tao;LIU Lingdi;TIAN Wei;LIU Ming;WEN Chunxiu(Institute of Cash Crops,Hebei Academy of Agriculture and Forestry Sciences,Shijiazhuang 050051,China)

机构地区：[1]河北省农林科学院经济作物研究所,河北石家庄050051

出　　处：《特产研究》2023年第6期1-5,共5页Special Wild Economic Animal and Plant Research

基　　金：河北省重点研发计划专项项目(22326301D);河北省农林科学院基本科研业务费项目(2021050203);财政部和农业农村部:国家现代农业产业技术体系资助项目(CARS-21)。

摘　　要：荆芥是我国常用大宗药材。为了研究荆芥基因组大小,本研究采用流式细胞术和K-mer分析方法对荆芥进行了基因组大小、GC含量、杂合度和重复序列评估。结果显示:基于流式细胞术,荆芥基因组平均大小为0.76Gb;采用K-mer分析显示,荆芥基因组大小为0.903 Gb,GC含量为38.77%,杂合率约为0.32%,重复序列约为66.93%;荆芥基因组拼接组装后contig总长为792215707 bp,contig N50为960 bp,scaffold总长为813473842 bp,scaffold N50为1650 bp。本研究结合流式细胞术和全基因组调查结果,分析评估荆芥基因组大小在0.7~0.9 Gb之间,基因组序列重复比例较高。本研究对荆芥基因组进行了初步的探索,为荆芥的基因组学研究提供了参考依据。Nepeta cataria is a common medicinal material in China.In order to study the genome size of Nepeta cataria,we evaluated the genome size,GC content,heterozygosity and repeat sequence of the germplasm resources of Nepeta cataria using flow cytometry and K-mer analysis.The results showed that the average genome size of Nepeta cataria was 0.76 Gb basing on flow cytometry.K-mer analysis showed that the genome size of Nepeta cataria was 0.903 Gb,GC content was 38.77%,heterozygosity rate was 0.32%,and repeat sequence was 66.93%.After genome assembly of Nepeta cataria,the total length of contig was 792,215,707 bp and contig N50 was 960 bp,and the total length of scaffold was 813,473,842 bp and scaffold N50 was 1650 bp.Combining with the results of flowcytometry and genome-wide investigation,the genome size of Nepeta cataria was estimated to be about 0.7~0.9 Gb with high sequence repetition ratio.This study conducted a preliminary exploration of the genome of Nepeta cataria,and provided a reference for the genomics research of Nepeta cataria.

关 键 词：荆芥 流式细胞术 K-mer 基因组大小 

分 类 号：S567.219[农业科学—中草药栽培] Q943.2[农业科学—作物学]