基于RNA-Seq技术的高牛鞭草与扁穗牛鞭草转录组de novo拼接及SSR分子标记的开发与利用
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- 英文论文题名：De novo transcriptome analysis and molecular marker development of two Hemarthria species based on RNA-Seq technology
- 论文作者：黄秀 ; 严海东 ; 张新全 ; 张健 ; Taylor P.Frazier ; 黄德均 ; 陆路 ; 黄琳凯 ; 刘伟 ; 彭燕 ; 马啸 ; 闫艳红
- 英文论文作者：Huang xiu ; Yan haidong ; Zhang xinquan ; Zhang jian ; Frazier taylor P ; Huang dejun ; Lu lu ; Huang linkai ; Liu wei ; Peng yan ; Ma xiao ; Yan yanhong ; Sichuan Agricultural University ; Animal Science and Technology College ; Department of Grassland Science ; Chongqing Academy of Animal Sciences ; Herbivorous Livestock Research Institute ; Virginia Polytechnic Institute and State University ; Department of Horticulture ; Universitat Autonoma de Barcelona ; Biosciences Faculty ; Department of Biochemistry and Molecular Biology
- 年：2016
- 作者机构：四川农业大学动物科技学院草业科学系;重庆市畜牧科学院草食牲畜研究所;弗吉尼亚理工大学园艺系;西班牙巴塞罗那自治大学生命科学学院生物化学与分子生物学系;
- 论文关键词：de novo组装 ; 分子标记开发 ; 牛鞭草属 ; RNA-Seq ; 转录组
- 英文论文关键词：De now assembly ; Marker development ; Hemarthria R ; Br ; RNA-Seq ; Transcriptome
- 会议召开时间：2016-05-25
- 会议录名称：第七届中国畜牧科技论坛论文集
- 英文会议录名称：Proceeding of the 7th China Animal Husbandry Sci-tech Forum
- 语种：中文
- 分类号：Q943.2;S54
- 学会代码：ZGXJ
- 会议名称：第七届中国畜牧科技论坛
- 会议地点：中国重庆
- 主办单位：中国畜牧兽医学会
- 学会名称：中国畜牧兽医学会
- 页数：9
- 文件大小：1792k
- 原文格式：O
- 会议级别：全国
摘要
(目的)本研究旨在挖掘牛鞭草基因资源,丰富其基因组信息。(方法)本研究采用Illumina HiSeq~(TM)2500高通量测序技术对高牛鞭草和扁穗牛鞭草材料的叶片或根系4个样本(T01、T02、T03和T04)进行转录组测序。(结果)结果表明,每个RNA样本获得了超过2400万条高质量reads。经过de novo组装后,‘雅安'和‘1110'材料分别获得了137142条和77150条unigenes,其中86731条unigenes(63.24%)和48645条unigenes(63.05%)被成功地注释功能。合并两个材料的unigenes后进行SSR位点检测,从8330个unigenes中,共检测得到10888个SSR位点。为了验证识别到的SSR位点,我们为此设计了高质量的SSR引物。从中随机选取了54对SSR引物进行验证,发现大多数这些引物能成功地扩增出期望的PCR产物。(结论)本研究两个材料获得的序列数据极大地丰富了牛鞭草可利用的基因组资源,并开发的SSR标记将进一步促进牛鞭草属植物在遗传育种和分子标记辅助选择等方面的研究进展。
(Objective) This study was to mine the genetic recources of Hemarthria R.Br.in order to enrich its genomic information.(Method) In this study,we used the Illumina HiSeq 2500 platform to perform a large-scale transcriptome analysis of leaves or roots consisting of four samples(T01,T02,T03 and T04) of H.compressa 'Yaan' and H.altissima'1110.(Result) Sequencing runs that used each samples yielded more than 24 million high-quality reads.After de novo assembly,137,142 and 77,150 unigeneswere obtained for'Yaan'and'1110',respectively.In addition,a total of 86,731 'Yaan' and 48,645 '1110' unigenes were successfully annotated.After consolidating the unigenes for both materials,10,888 SSRs were identified in 8,330 unigenes.To validate the identified markers,high quality PCR primers were designed for SSRs.We randomly tested 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product.The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.
(Objective) This study was to mine the genetic recources of Hemarthria R.Br.in order to enrich its genomic information.(Method) In this study,we used the Illumina HiSeq 2500 platform to perform a large-scale transcriptome analysis of leaves or roots consisting of four samples(T01,T02,T03 and T04) of H.compressa 'Yaan' and H.altissima'1110.(Result) Sequencing runs that used each samples yielded more than 24 million high-quality reads.After de novo assembly,137,142 and 77,150 unigeneswere obtained for'Yaan'and'1110',respectively.In addition,a total of 86,731 'Yaan' and 48,645 '1110' unigenes were successfully annotated.After consolidating the unigenes for both materials,10,888 SSRs were identified in 8,330 unigenes.To validate the identified markers,high quality PCR primers were designed for SSRs.We randomly tested 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product.The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.
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