De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

文献类型： 外文期刊

第一作者： Li, Dejun

作者： Li, Dejun;Deng, Zhi;Qin, Bi;Liu, Xianghong;Men, Zhonghua

作者机构：

关键词： Rubber tree;Transcriptome;EST-SSR;Illumina paired-end sequencing;de novo assembly;Bark

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2012 年 13 卷

页码：

收录情况： SCI

摘要： Background: In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. Results: In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO) and Clusters of Orthologous Group (COG). When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%), suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. Conclusion: By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research generated a substantial fraction of rubber tree transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation, and microarrays development in rubber tree. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding in rubber tree. Moreover, this study also supported that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for transcriptome characterization and molecular marker development in non-model species, especially those with large and complex genomes.

分类号：

  • 相关文献

[1]Characterization of the global transcriptome using Illumina sequencing and novel microsatellite marker information in seashore paspalum. Jia, Xinping,Deng, Yanming,Sun, Xiaobo,Liang, Lijian,Ye, Xiaoqing.

[2]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

[3]De novo assembly of the transcriptome of Neottopteris nidus using Illumina paired-end sequencing and development of EST-SSR markers. Jia, Xinping,Deng, Yanming,Sun, Xiaobo,Liang, Lijian,Su, Jiale.

[4]Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Wang, Shufen,He, Qiwei,Liu, Xianxian,Xu, Wenling,Li, Libin,Gao, Jianwei,Wang, Fengde,Wang, Xiufeng. 2012

[5]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

[6]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

[7]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

[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]De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development. Chen, Honglin,Wang, Lixia,Liu, Xiaoyan,Hu, Liangliang,Wang, Suhua,Cheng, Xuzhen. 2017

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

[12]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.

[13]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.

[14]Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. Gebelin, Virginie,Argout, Xavier,Engchuan, Worrawat,Pitollat, Bertrand,Duan, Cuifang,Montoro, Pascal,Leclercq, Julie,Engchuan, Worrawat,Duan, Cuifang. 2012

[15]Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD). Liu, Jin-Ping,Tian, Xiao-Yan,Xia, Zhi-Qiang,Li, Yi-Jian. 2015

[16]Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex. Wei, Fang,Luo, Shigiao,Zheng, Qiankun,Qiu, Jian,Yang, Wenfeng,Wu, Ming,Xiao, Xianzhou.

[17]De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. Long, Yan,Zhang, Jingwen,Tian, Xinjie,Wu, Shanshan,Pei, Xin Wu,Zhang, Qiong,Zhang, Jianping,Dang, Zhanhai. 2014

[18]Transcriptome analysis between invasive Pomacea canaliculata and indigenous Cipangopaludina cahayensis reveals genomic divergence and diagnostic microsatellite/SSR markers. Mu, Xidong,Song, Hongmei,Luo, Du,Gu, Dangen,Xu, Meng,Luo, Jianren,Hu, Yinchan,Hou, Guangyuan,Xu, Peng,Zhang, Jiaen. 2015

[19]De Novo Characterization of Leaf Transcriptome Using 454 Sequencing and Development of EST-SSR Markers in Tea (Camellia sinensis). Wu, Hualing,Chen, Dong,Li, Jiaxian,Qiao, Xiaoyan,Huang, Hualin,He, Yumei,Wu, Hualing,Chen, Dong,Li, Jiaxian,Qiao, Xiaoyan,Huang, Hualin,He, Yumei,Yu, Bo.

[20]De novo assembly and characterization of the root transcriptome and development of simple sequence repeat markers in Paphiopedilum concolor. Li, D. M.,Zhao, C. Y.,Liu, X. R.,Liu, X. F.,Lin, Y. J.,Liu, J. W.,Chen, H. M.,Lu, F. B.. 2015

作者其他论文 更多>>

微信小程序