甘薯近緣野生種Ipomoea Littoralis全基因組Survey分析

霍愷森 曹清河 王珧 陳艷麗 朱國(guó)鵬

摘 ?要Ipomoea littoralis是甘薯的近緣野生種之一，對(duì)其全基因組的研究可為甘薯種質(zhì)資源的創(chuàng)新提供參考，同時(shí)為全基因組精細(xì)圖譜的繪制打下基礎(chǔ)。本研究通過(guò)二代高通量測(cè)序技術(shù)（Illumina Hiseq 2500），測(cè)序深度約為60?，經(jīng)過(guò)濾后得到22.45 G數(shù)據(jù)，結(jié)合生物信息學(xué)手段估算基因組大小、雜合率、重復(fù)序列和GC含量等基因組特征。預(yù)估基因組大小經(jīng)修正后為676.27?Mb。K-mer分析結(jié)果得出I.littoralis基因組中重復(fù)序列所占比率為60.98%，雜合率為0.81%;初步組裝結(jié)果，contigs N50為0.684 kb，總讀長(zhǎng)為0.538 Gb，scaffolds N50為12.09 kb，總讀長(zhǎng)為0.602?Gb;GC平均深度及含量分布出現(xiàn)分層現(xiàn)象。本研究首次報(bào)道I.littoralis的基因組特征信息，為進(jìn)一步全基因組深度測(cè)序提供參考。

關(guān)鍵詞 ?甘薯;基因組調(diào)查;Ipomoea littoralis;種質(zhì)資源中圖分類(lèi)號(hào)??S531??????文獻(xiàn)標(biāo)識(shí)碼??A

Genome Survey Analysis of Relative Wild Species Ipomoea Littoralis?in Sweetpotato

HUO?Kaisen^1，2， CAO?Qinghe²， WAND?Yao¹，?CHEN?Yanli^1*，ZHU?Guopeng¹

1. College of Horticulture，?Hainan University，?Haikou， Hainan 570228， China; 2. Xuzhou Institute of Agriculture， Xuzhou， Jiangsu 221131， China

Abstract ?Ipomoea littoralisis one of the wild relatives of sweet potato. Its genome-wide research can provide reference for the innovation of sweet potato germplasm resources and for the mapping of the whole genome.This study used a second-generation high-throughput sequencing technology （Illumina Hiseq 2500） with a sequencing depth of approximately 60??and filtered to obtain 22.45 G data. Bioinformatics was used to estimate genome size， heterozygosity， repeat sequence and GC. The predicted genome size was 676.27 Mb. The K-mer analysis showed that the ratio of repeats was 60.98%， and the heterozygosity rate was 0.81%. The contigs N50 was 684 kb after preliminary assembly. The total reading length was 0.538 Gb， scaffolds N50 was 12.09 kb， and the total reading length was 0.602 Gb. The average depth and content distribution of GC were stratified.

Keywords ?sweet?photo; genome survey;Ipomoea littoralis; germplasm resources

DOI10.3969/j.issn.1000-2561.2019.10.012

甘薯[Ipomoea batatas（L.） Lam]是旋花科（Convolvulaceae）甘薯屬（Ipomoea）植物，在亞、非、拉美等熱帶及亞熱帶地區(qū)廣為栽培，是一種重要的糧食、蔬菜、工業(yè)原料作物及新型能源作物^[1]。而Ipomoea littoralis作為甘薯的近緣野生種之一，可能攜帶大量的優(yōu)異基因，對(duì)甘薯種質(zhì)資源的創(chuàng)新具有重要意義。植物的基因組反應(yīng)了生物的全部的、特定的遺傳信息，從根本上決定了遺傳物質(zhì)的傳遞。基因組含量又稱(chēng)為C值，是指一個(gè)物種單倍體核的DNA含量^[2]。同一物種的基因組含量是穩(wěn)定的， 也是各個(gè)物種固有的特征參數(shù)^[3]。相對(duì)于缺乏基因組數(shù)據(jù)的非模式資源植物來(lái)看，基因組特征的研究是分子機(jī)理研究和植物基因資源開(kāi)發(fā)的前提^[4]。在對(duì)基因組大小的檢測(cè)技術(shù)從復(fù)性動(dòng)力學(xué)估算法^[5]，到脈沖凝膠電泳法^[6]，到流式細(xì)胞法^[7]，再到現(xiàn)在的高通量測(cè)序K-mer估計(jì)法^[8]。……