甘薯近缘种Ipomoeacordatotriloba基因组大小测定及高通量调查测序

王珧 邓逸桐 戴习彬 张安 曹清河 陈艳丽

摘  要：利用流式细胞术，以大豆Williams 82为内参，对甘薯近缘野生种Ipomoea cordatotriloba进行基因组大小测定，结合染色体压片技术进行倍性鉴定，并利用二代高通量测序技术对测定结果进行验证。结果表明：利用流式细胞术测得I. cordatotriloba基因组大小为（539.69±13.76）Mb;染色体压片结果显示其染色体数目为30条，由于其基数x=15，从而获知I. cordatotriloba為二倍体;经K-mer计算并修正后得出的C值为560.70 Mb，与流式细胞分析结果相近;同时，测序结果显示其基因组杂合率为0.40%;重复序列比率为57.93%;GC含量为38.10%。以上结果为此物种全基因组精细图谱绘制打下基础，同时为甘薯近缘野生种的利用提供参考。

关键词：甘薯;Ipomoea cordatotriloba;基因组大小;流式细胞法;K-mer计算中图分类号：S531;Q75      文献标识码：A

DNA Amount Estimation and Genome Survey of Sweetpotato Wild RelativesIpomoea cordatotriloba

WANG Yao^{1， 2}， DENG Yitong²， DAI Xibin²， ZHANG An²， CAO Qinghe²， CHEN Yanli^1*

1. College of Horticulture， Hainan University， Haikou， Hainan 570228， China; 2. Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences， Xuzhou， Jiangsu 221131， China

Abstract： DNA content of sweetpotato wild relativesIpomoea cordatotrilobawas determinated by flow cytometry using soybeanWilliams 82 as the internal reference in this study. The ploidy was determined by chromosome counting. In order to verify the reliability of the results， the next-generation sequencing was used to further test and verify. It was a diploid species with base number was 15. The genome size was （539.69±13.76） Mb by the flow cytometry analysis. The C-value determined by sequencing was similar to the results of flow cytometry. Furthermore， the genomic heterozygosity rate， repeat sequence ratio and GC content was 0.40%， 57.93% and 38.10%， respectively. The above results would lay the foundation for the whole genome sequencing and assemble of this species， and provide references for the utilization of sweetpotato relatives.

Keywords： sweetpotato;Ipomoea cordatotriloba; genome size; flow cytometry; sequencing

DOI： 10.3969/j.issn.1000-2561.2020.06.012

甘薯因具有营养丰富、适应性广等优点大面积种植于热带、亚热带地区^[1]，是世界第七大主粮作物（FAO，2018）。甘薯属植物约有800～900个种，其中有二倍体、四倍体和六倍体等不同倍性的物种资源，且许多野生种具有优良的抗性基因^[2-3]。基因组特征研究是植物基因资源开发、利用的前提。基因组大小、重复序列比例、杂合率和GC含量等参数会影响基因组的拼接组装过程^[4]。基因组大小是指物种单倍体所含的DNA量，是表征生物基因组多样性的基本参数^[5]。目前测定基因组大小的方法很多，流式细胞法（Flow cytometry，FCM）因其快速、准确的特点而被广泛应用^[6]，超过80%的物种都是采用该方法进行基因组大小测定^[7]，如枣、月季、草莓、灵芝^[8-11]等。近年来，采用低深度测序后进行K-mer分析也是常用方法之一^[12]。……