您好，欢迎访问中国水产科学研究院 机构知识库！
中国水产科学研究院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

文献类型： 外文期刊

作者： Wang, Jin-Tu 1 ; Li, Jiong-Tang 1 ; Zhang, Xiao-Feng 3 ; Sun, Xiao-Wen 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

2.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

3.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Haerbin 150070, Peoples R China

关键词： Sequence assembly;Genome duplication;Common carp;Substitution rate;Speciation

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: Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event. Results: We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp. Conclusions: The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.

  • 相关文献

[1]Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family. Zhang, Yan,Liang, Liqun,Jiang, Peng,Li, Dayu,Lu, Cuiyun,Sun, Xiaowen,Zhang, Yan,Jiang, Peng,Li, Dayu. 2008

[2]Evolution of the viral hemorrhagic septicemia virus: Divergence, selection and origin. He, Mei,Liang, Yang,Teng, Chun-Bo,Yan, Xue-Chun,Sun, Xiao-Wen.

[3]Dating the divergence of the infectious hematopoietic necrosis virus. He, Mei,Teng, Chun-Bo,Ding, Nai-Zheng,He, Cheng-Qiang,Yan, Xue-Chun.

[4]Predicted Body Weight of Progeny Obtained by a Three-Way Cross and Back Cross Based on a 3 × 3 Complete Diallel Cross of Common Carp (Cyprinus carpi). Shengyan Su,Zaijie Dong,Xuebin Li,Xinhua Yuan,Pao Xu,Zhuang Xie. 2011

[5]Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations. Liu, Gangbiao,Zou, Yangyun,Su, Zhixi,Liu, Gangbiao,Zou, Yangyun,Gu, Xun,Su, Zhixi,Cheng, Qiqun,Zeng, Yanwu,Gu, Xun.

[6]Molecular characterization, origin, and evolution of teleost p68 gene family: Insights from Japanese flounder, Paralichthys olivaceus. Wang, Zhongkai,Wang, Zhongkai,Liu, Wei,Zhou, Nayu,Wang, Huizhen,Li, Peizhen,Wang, Mengxun,Zhang, Quanqi.

[7]SPECIATION AND ASSESSMENT OF HEAVY METAL IN SEDIMENTS FROM A TYPICAL MARICULTURE BASE IN GUANGDONG COAST, CHINA. Gu, Yangguang,Lin, Qin,Wang, Zenghuan,Wang, Xunuo,Gu, Yangguang,Yang, Yufeng,Jiang, Shijun. 2011

[8]Speciation of Polyploid Cyprinidae Fish of Common Carp, Crucian Carp, and Silver Crucian Carp Derived from Duplicated Hox Genes. Yuan, Jian,He, Zhuzi,Yuan, Xiangnan,Jiang, Xiayun,Zou, Shuming,Sun, Xiaowen.

[9]Biotransformation and detoxification of inorganic arsenic in Bombay oyster Saccostrea cucullata. Zhang, Wei,Guo, Zhiqiang,Zhou, Yanyan,Zhang, Li,Zhou, Yanyan,Liu, Huaxue.

[10]A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs. Zheng, Xianhu,Kuang, Youyi,Zhang, Xiaofeng,Lu, Cuiyun,Cao, Dingchen,Li, Chao,Sun, Xiaowen,Zheng, Xianhu. 2011

[11]High Throughput Mining and Characterization of Microsatellites from Common Carp Genome. Ji, Peifeng,Zhang, Yan,Zhao, Zixia,Wang, Jian,Li, Jiongtang,Xu, Peng,Sun, Xiaowen,Li, Chao,Sun, Xiaowen. 2012

[12]Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). Xu, Jian,Zhao, Zixia,Li, Jiongtang,Jiang, Yanliang,Zhang, Yan,Li, Qiang,Zhu, Yuanyuan,Liu, Yuanyuan,Xu, Peng,Sun, Xiaowen,Zhang, Xiaofeng,Zheng, Xianhu,Kuang, Youyi,Sun, Xiaowen,Feng, Jianxin,Li, Chuangju,Yu, Juhua,Xu, Peng. 2014

[13]Use and exchange of aquatic resources relevant for food and aquaculture: common carp (Cyprinus carpio L.). Jeney, Zsigmond,Jian, Zhu. 2009

[14]Development of MHC Class I and II B Primers in Common Carp and its Molecular Characterization. Jia, Zhiying,Chi, Xifeng,Li, Chitao,Shi, Lianyu,Chi, Xifeng. 2010

[15]Accumulation, histopathological effects and response of biochemical markers in the spleens and head kidneys of common carp exposed to atrazine and chlorpyrifos. Wang, Xu,Xing, Houjuan,Jiang, Yan,Xu, Shiwen,Xing, Houjuan,Sun, Gang,Wu, Hongda,Xu, Qiyou. 2013

[16]A Consensus Linkage Map Provides Insights on Genome Character and Evolution in Common Carp (Cyprinus carpio L.). Zhang, Xiaofeng,Zheng, Xianhu,Kuang, Youyi,Li, Chao,Cao, Dingchen,Lu, Cuiyun,Sun, Xiaowen,Zhang, Yan,Zhao, Zixia,Zhao, Lan,Jiang, Li,Xu, Peng. 2013

[17]Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. Zhu, Ya-Ping,Xue, Wei,Wang, Jin-Tu,Wan, Yu-Mei,Xu, Peng,Zhang, Yan,Li, Jiong-Tang,Sun, Xiao-Wen,Zhu, Ya-Ping,Xue, Wei,Wang, Jin-Tu,Wang, Shao-Lin. 2012

[18]A genetic linkage map of common carp (Cyprinus carpio L.) And mapping of a locus associated with cold tolerance. Sun, XW,Liang, LQ. 2004

[19]Genome-wide characterization of Toll-like receptor gene family in common carp (Cyprinus carpio) and their involvement in host immune response to Aeromonas hydrophila infection. Gong, Yiwen,Feng, Shuaisheng,Li, Shangqi,Zhang, Yan,Zhao, Zixia,Jiang, Yanliang,Gong, Yiwen,Hu, Mou,Jiang, Yanliang,Xu, Peng. 2017

[20]Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes. Dong, Chuanju,Xu, Jian,Wang, Baosen,Sun, Xiaowen,Xu, Peng,Dong, Chuanju,Xu, Jian,Wang, Baosen,Sun, Xiaowen,Xu, Peng,Dong, Chuanju,Feng, Jianxin,Jeney, Zsigmond.

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：中国水产科学研究院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台