De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development

文献类型： 外文期刊

第一作者： Chen, Honglin

作者： Chen, Honglin;Wang, Lixia;Liu, Xiaoyan;Hu, Liangliang;Wang, Suhua;Cheng, Xuzhen

作者机构：

关键词： Vigna unguiculata (L.) Walp;Transcriptome;De novo assembly;Functional annotation;Genic SSR

期刊名称：BMC GENETICS （ 影响因子：2.797； 五年影响因子：3.263 ）

ISSN： 1471-2156

年卷期： 2017 年 18 卷

页码：

收录情况： SCI

摘要： Background: Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. Results: Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions. Conclusions: This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

分类号：

  • 相关文献

[1]De novo sequencing and characterization of the Bradysia odoriphaga (Diptera: Sciaridae) larval transcriptome. Chen, Haoliang,Lin, Lulu,Xie, Minghui,Zhang, Guangling,Su, Weihua.

[2]A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Liu, Xiaohui,Lu, Tingting,Yu, Shuliang,Li, Ying,Huang, Yuchen,Huang, Tao,Zhang, Lei,Zhu, Jingjie,Zhao, Qiang,Fan, Danlin,Mu, Jie,Shangguan, Yingying,Feng, Qi,Guan, Jianping,Ying, Kai,Zhang, Yu,Lin, Zhixin,Sun, Zongxiu,Qian, Qian,Lu, Yuping,Han, Bin.

[3]De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites. Sun, Xiujun,Li, Dongming,Liu, Zhihong,Zhou, Liqing,Wu, Biao,Yang, Aiguo,Sun, Xiujun,Li, Dongming,Liu, Zhihong,Zhou, Liqing,Wu, Biao,Yang, Aiguo. 2017

[4]De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissue. Wu, Shuanghua,Lei, Jianjun,Chen, Guoju,Cao, Bihao,Chen, Changming,Chen, Hancai. 2017

[5]De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes. He, Bin,Gu, Yinghong,Cheng, Xiaojie,Wei, Changhe,Zhang, Yizheng,Tao, Xiang,Fu, Jian,Cheng, Zaiquan. 2015

[6]De novo assembly, gene annotation, and marker development of mulberry (Morus atropurpurea) transcriptome. Dai, Fanwei,Tang, Cuiming,Wang, Zhenjiang,Luo, Guoqing,He, Li,Yao, Liuhui. 2015

[7]De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). Li, Dejun,Deng, Zhi,Qin, Bi,Liu, Xianghong,Men, Zhonghua. 2012

[8]DE NOVO TRANSCRIPTOME ANALYSIS OF MULBERRY (MORUS L.) UNDER DROUGHT STRESS USING RNA-SEQ TECHNOLOGY. Wang, Heng,Tong, Wei,Feng, Li,Jiao, Qian,Long, Li,Fang, Rongjun,Zhao, Weiguo,Long, Li,Zhao, Weiguo,Fang, Rongjun,Zhao, Weiguo.

[9]De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries). Yue, Y. J.,Yang, B. H.,Yue, Y. J.,Liu, J. B.,Yang, M.,Han, J. L.,Guo, T. T.,Guo, J.,Feng, R. L.,Yang, B. H.. 2015

[10]Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Napier Grass (Pennisetum purpureum Schum). Wang, Jia,Hu, Zhongli,Diao, Ying,Chen, Zhitong,Huang, Yibing,Jin, Surong.

[11]RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Xia, Zhihui,Xu, Huimin,Zhai, Jinling,Luo, Hongli,He, Chaozu,Huang, Xi,Li, Dejun.

[12]Genetic diversity a population structure analysis of a accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. Chen, Honglin,Hu, Liangliang,Wang, Lixia,Wang, Suhua,Cheng, Xuzhen,Chen, Hong,Wang, Ming Li. 2017

[13]TRANSCRIPTOMIC ANALYSIS, GENIC SSR DEVELOPMENT, AND GENETIC DIVERSITY OF PROSO MILLET (PANICUM MILIACEUM; POACEAE). Hou, Siyu,Sun, Zhaoxia,Li, Yaoshen,Wang, Yijie,Ling, Hubin,Xing, Guofang,Han, Yuanhuai,Li, Hongying,Hou, Siyu,Xing, Guofang,Han, Yuanhuai. 2017

[14]CottonFGD: an integrated functional genomics database for cotton. Zhu, Tao,Liang, Chengzhen,Meng, Zhigang,Sun, Guoqing,Meng, Zhaoghong,Guo, Sandui,Zhang, Rui. 2017

[15]Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data. Zhao, Qing-bo,Sun, Hao,Zhang, Zhe,Wang, Qi-shan,Zhang, Xiang-zhe,Pan, Yu-chun,Liao, Rong-rong,Yang, Chang-suo,Wang, Qi-shan,Zhang, Xiang-zhe,Pan, Yu-chun. 2018

[16]PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics. Shu, Changlong,Zhang, Jie,Schmidt, Emily,Li, Pei,Lenox, Douglas,Liu, Lin,Liang, Chun,Schmidt, Emily,Lenox, Douglas,Liang, Chun. 2012

[17]Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs. Sha, Ai-Hua,Li, Chen,Yan, Xiao-Hong,Shan, Zhi-Hui,Zhou, Xin-An,Jiang, Mu-Lan,Mao, Han,Chen, Bo,Wan, Xia,Wei, Wen-Hui.

[18]De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways. Bai, Yu,Zhou, Ying,Tang, Xiaoqing,Wang, Yu,Wang, Fangquan,Yang, Jie. 2018

[19]Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development. Wei, Zunzheng,Zhang, Qixiang,Wei, Zunzheng,Zhang, Qixiang,Wei, Zunzheng,Xiong, Min,Wang, Xian,Zhou, Di,Sun, Zhenzhen,Cui, Binbin. 2016

[20]High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica. Qi, Weicong,Lin, Feng,Zhao, Han,Liu, Yuhe,Huang, Bangquan,Cheng, Jihua,Zhang, Wei. 2016

作者其他论文 更多>>

微信小程序