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Nature genetics
Nov, 2014;46 (11): 1212-9.

Genome sequence and genetic diversity of the common carp, Cyprinus carpio.

Peng Xu, Xiaofeng Zhang, Xumin Wang, Jiongtang Li, Guiming Liu, Youyi Kuang, Jian Xu, Xianhu Zheng, Lufeng Ren, Guoliang Wang, Yan Zhang, Linhe Huo, Zixia Zhao, Dingchen Cao, Cuiyun Lu, Chao Li, Yi Zhou, Zhanjiang Liu, Zhonghua Fan, Guangle Shan, Xingang Li, Shuangxiu Wu, Lipu Song, Guangyuan Hou, Yanliang Jiang, Zsigmond Jeney, Dan Yu, Li Wang, Changjun Shao, Lai Song, Jing Sun, Peifeng Ji, Jian Wang, Qiang Li, Liming Xu, Fanyue Sun, Jianxin Feng, Chenghui Wang, Shaolin Wang, Baosen Wang, Yan Li, Yaping Zhu, Wei Xue, Lan Zhao, Jintu Wang, Ying Gu, Weihua Lv, Kejing Wu, Jingfa Xiao, Jiayan Wu, Zhang Zhang, Jun Yu, Xiaowen Sun
Author Information
  1. Peng Xu: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  2. Xiaofeng Zhang: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  3. Xumin Wang: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  4. Jiongtang Li: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  5. Guiming Liu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  6. Youyi Kuang: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  7. Jian Xu: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  8. Xianhu Zheng: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  9. Lufeng Ren: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  10. Guoliang Wang: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  11. Yan Zhang: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  12. Linhe Huo: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  13. Zixia Zhao: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  14. Dingchen Cao: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  15. Cuiyun Lu: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  16. Chao Li: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  17. Yi Zhou: Stem Cell Program, Division of Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
  18. Zhanjiang Liu: 1] Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China. [2] Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, USA.
  19. Zhonghua Fan: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  20. Guangle Shan: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  21. Xingang Li: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  22. Shuangxiu Wu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  23. Lipu Song: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  24. Guangyuan Hou: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  25. Yanliang Jiang: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  26. Zsigmond Jeney: Research Institute for Fisheries, Aquaculture and Irrigation, Szarvas, Hungary.
  27. Dan Yu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  28. Li Wang: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  29. Changjun Shao: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  30. Lai Song: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  31. Jing Sun: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  32. Peifeng Ji: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  33. Jian Wang: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  34. Qiang Li: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  35. Liming Xu: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  36. Fanyue Sun: Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, USA.
  37. Jianxin Feng: Henan Academy of Fishery Science, Zhengzhou, China.
  38. Chenghui Wang: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
  39. Shaolin Wang: Department of Psychiatry and Neurobiology Science, University of Virginia, Charlottesville, Virginia, USA.
  40. Baosen Wang: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  41. Yan Li: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  42. Yaping Zhu: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  43. Wei Xue: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  44. Lan Zhao: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  45. Jintu Wang: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
  46. Ying Gu: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  47. Weihua Lv: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
  48. Kejing Wu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  49. Jingfa Xiao: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  50. Jiayan Wu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  51. Zhang Zhang: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  52. Jun Yu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  53. Xiaowen Sun: 1] Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China. [2] Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
PMID: 25240282 DOI: 10.1038/ng.3098

Abstract

The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

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MeSH Term

Animals
Base Sequence
Carps
Chromosome Mapping
Evolution, Molecular
Gene Expression Profiling
Genetic Variation
Genome
Genome Components
Molecular Sequence Data
Sequence Analysis, DNA
Skin
Species Specificity
Journal Article Research Support, Non-U.S. Gov't

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