摘要
马鞍藤(Ipomoea pes-caprae(L.)R. Br.)是甘薯的近缘野生种之一,为热带、亚热带海滩生长的多年生藤蔓植物,作为沿海地区的园林绿化植物之一,具有较强的耐盐性。马鞍藤基因组学的研究可为耐盐甘薯种质创制提供信息参考。本试验调查了马鞍藤基因组大小和特征概况,为后续全基因组精细图谱绘制打下基础。研究以已知基因组大小的三裂叶薯(Ipomoea triloba L.)为对照,运用流式细胞术对马鞍藤基因组大小进行初步预估;使用二代高通量测序技术(Illumina Hiseq2500)对马鞍藤基因组进行survey评估,测序深度30×,利用生物信息学方法估算马鞍藤GC含量(即鸟嘌呤和胞嘧啶所占比例)、杂合率、重复序列等基因组概况。结果表明:流式细胞术估算马鞍藤基因组大小为1012.704±17.37 Mb;经全基因组Survey测定获得马鞍藤有效数据为21.71 Gb,基因组大小经修正后估算为1041.65 Mbp;通过K-mer分布曲线估算马鞍藤基因组中重复序列所占比率为74.52%,杂合率为0.99%;经初步组装后,GC平均深度及含量分布存在异常,出现分层的现象,这可能与马鞍藤基因组杂合率较高有关。本试验首次报导甘薯属耐盐植物马鞍藤基因组大小及特征信息,为马鞍藤进一步的全基因组深度测序和甘薯耐盐基因挖掘打下基础。
Ipomoea pes-caprae(L.)R. Br. is one of the perennial wild species of sweetpotato,a perennial vine plant which grows on tropical and subtropical beaches. It is one of the landscaping plants in coastal areas with strong salt tolerance. The study of Ipomoea pes-caprae(L.)R.Br. genome-wide can provide reference for the improvement of salt-tolerant varieties of Sweetpotato and the innovation of salt-tolerant sweet potato germplasm resources. In order to reduce the blindness of whole-genome deep sequencing,this experiment aims to understand the genome overview and provide insight for the following mapping of the whole genome. We performed the experiments in preliminary estimation of the genome size of Ipomoea pes-caprae(L.)R.Br. by ?ow cytometry,generation of highthroughput sequencing datasets,and the bioinformatics analysis of genomic pro?les such as Ipomoea pes-caprae(L.)R.Br. GC content,heterozygosity,and repeat sequences. The results showed that the genomic size by using the?ow cytometry was 1012.99 Mb,and the clean data of Ipomoea pes-caprae was(L.)R.Br. 21.71 Gb by genomewide Survey. By integrated analysis with 30× genomic dataset,its genome size was re-estimated to be 1041.65 Mb. K-mer analysis suggested 74.52% of repeated sequences of the Ipomoea pes-caprae(L.)R.Br. genome. The heterozygosity rate was 0.99%. The initial depth of GC and the content distribution were abnormal after initial assembly. The stratification phenomenon may be related to the high heterozygous rate of the Ipomoea pes-caprae(L.)R.Br. genome. Thus,this work reported the preliminary information of the Ipomoea pes-caprae(L.)R.Br. genome,which lays a foundation for further genome-wide deep sequencing and salt tolerance gene mining.
作者
霍恺森
赵冬兰
陈艳丽
周志林
王珧
唐君
朱国鹏
曹清河
HUO Kai-sen;ZHAO Dong-lan;CHEN Yan-li;ZHOU Zhi-lin;WANG Yao;TANG Jun;ZHU Guo-peng;CAO Qing-he(Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences, Xuzhou 221131;Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228)
出处
《植物遗传资源学报》
CAS
CSCD
北大核心
2019年第3期728-735,共8页
Journal of Plant Genetic Resources
基金
国家甘薯产业技术体系资源评价岗(CARS-10-B1-2017)
国家自然科学基金(31461143017)
国家农作物种质资源平台徐州甘薯平台(NICGR-062)
江苏省重点研发项目(BE2016394)~~
关键词
马鞍藤
流式细胞术
基因组测序
GC含量
杂合度
重复序列
Ipomoea pes-caprae(L.)R.Br.
flow cytometry
genome sequencing
GC content
heterozygosity
repetitive sequences
