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罗汉果全基因组 Survey 分析

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  • 国家科技期刊平台
  • NETL
  • NSTL
  • 万方数据
罗汉果是广西特有药用及甜料植物，其主要成分之一甜苷 V 作为天然、非糖甜味剂，具有广阔的开发前景，但罗汉果目前完全来自于栽培，适生区狭窄，连作障碍严重，加之含量低导致甜苷 V 生产成本居高不下，严重限制了其应用。为了减少盲目性，在大规模全基因组深度测序之前，先做低覆盖度的基因组 Survey测序，评价基因组的大小及复杂程度，以确定适合该植物全基因组的测序研究策略。该研究采用第二代高通量测序技术(Illumina HiseqTM 2000)首次测定了罗汉果基因组大小，并利用生物信息学方法估计罗汉果杂合率、重复序列和 GC 含量等基因组信息。结果表明：(1)获得了18．1 Gb 罗汉果基因组测序数据，基因组大小估计为344．95 Mb 左右，测序深度为52×；(2)从 K-mer 分布曲线发现罗汉果基因组有明显的杂合峰，杂合率达1．5％，基因组高杂合导致组装的结果中 Contig N50和 Scaffold N50的长度比预期的要短很多，还造成 GC 平均深度及含量分布明显异常，存在一个低深度分布区域。基因组主峰后面有微弱的重复峰，说明罗汉果存在较多的重复序列；(3)由于罗汉果存在高杂合率和重复序列较多的特点，该基因组测序分析仅采用全基因组鸟枪法(WGS)策略不合适，为了更好地对全基因组进行序列拼接和组装，可尝试结合采用 Fosmid-to-Fosmid 或BAC-to-BAC 策略。该研究结果对于揭示罗汉果产量、有效成分含量、发育及抗病虫的分子机制，以及通过分子育种来提高甜苷 V 含量和降低生产成本具有重要意义，为全基因组测序策略的选择提供了依据。
Genome survey analysis in Siraitia grosvenorii
Siraitia grosvenorii (Luohanguo)is a herbaceous perennial medicinal and sweetener plant native in Guan-gxi of China.It has long been used in traditional Chinese medicine as a natural sweetener and also as a folk medicine for the treatment of lung congestion,colds and sore throats.Many cucurbitane-type triterpene glycosides have been i-solated and characterized from S .grosvenorii .The active components responsible for the sweetness are the mogro-sides,which are members of the family of triterpene glycosides.Mogroside V has an important prospect as natural and low calorie sweetener,which is nearly 425 times sweeter than sucrose.S .grosvenorii currently depends totally on cultivation in China.It’s limitedly applied because the narrow distribution,serious continuous cropping obstacle, low content and high extraction costs of mogroside V.In order to reduce blindness research and determine the appro-priate sequencing strategy,the genome survey before large-scale genome sequencing is needed.This survey can pro-vide information about the size and complexity of the whole genome of the S .grosvenorii .The next generation se-quencing technology which has been emerged as a cost effective approach for high-through-put sequence determination has dramatically improved the efficiency and speed of genes discovery and genome research.Genome sequencing of S . grosvenorii has the vital significance to reveal the molecular mechanism of yield,content,growth,pest and disease resistance,and provides an efficient approach to improve content and reduce cost of mogroside V by molecular breed-ing.In this study,the genome size of S .grosvenorii was determined by next-generation sequencing technologies (NGS,Illumina HiseqTM 2000).The hybridity percentage,repeats,and GC depth were also estimated by bioinfor-matics analysis.The results were as follows:(1)Two DNA libraries of 170 bp and 500 bp are constructed.After cleaning and quality checks,more than 18.1 Gb high quality data from the genome is generated,which were assem-bled into 943 296 contigs and 433 325 scaffolds by SOAP denovo software.The contig and scaffold numbers of the length more than 2 kb were 17 855 and 27 993 separately.The longest length of contig and scaffold were 29 kb and 268 kb.The N50 length of contig and scaffold were 484 bp and 2 331 bp.The average genome size and sequencing coverage depth of S .grosvenorii was about 344.95 Mb and 52 times respectively;(2)The genome of S .grosvernrii had obvious hybridity peak by K-mer method,the hybridity percentage as high as 1.5%.The assembly results showed that the length of contig N50 and scaffold N50 are much shorter than expected.High hybridity percentage of the genome leads to apparently unusual phenomenon between average depth and GC content,and had a low depth distribution area.There was a weak repeat peak behind the main peak,which demonstrated that S .grosvenorii has more repetitive sequences;(3)Whole-genome shotgun sequencing (WGS)should not be used to S .grosvenorii ge-nome sequencing separately,and the Fosmid-to-Fosmid or BAC-to-BAC library could be combinational used for bet-ter results.This study would not only obtain the basic resources of genome,but also provide a theoretical basis and target genes for S .grosvenorii in transgenic breeding and genetic engineering.

Siraitia grosvenorii (Luohanguo)genome sequencinghybridity percentageGC depthwhole-genome shotgun sequencing

唐其、马小军、莫长明、潘丽梅、韦荣昌、赵欢

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湖南农业大学 园艺园林学院，长沙 410128

广西药用植物园，南宁 530023

中国医学科学院 药用植物研究所，北京 100193

罗汉果 基因组测序 杂合率 GC 含量 鸟枪法测序策略

国家自然科学基金国家自然科学基金国家科技支撑计划项目广西农业科技成果转化项目广西自然科学基金湖南省科技计划重点项目广西卫生厅中医药科技专项

81373914314002752011BAI01B03桂科转1123013-122013GXNSFBA0191702014SK2005GZPT1235

2015

10.11931/guihaia.gxzw201404041

广西植物
广西壮族自治区广西植物研究所,中国科学院广西植物研究所,广西植物学会

广西植物

CSTPCDCSCD北大核心
影响因子：0.719
ISSN：1000-3142
年,卷(期)：2015.(6)
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