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Nat Genet. 2014 Nov;46(11):1212-9. doi: 10.1038/ng.3098. Epub 2014 Sep 21.

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

Author information

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.
3
Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
4
Stem Cell Program, Division of Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
5
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.
6
Research Institute for Fisheries, Aquaculture and Irrigation, Szarvas, Hungary.
7
Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, USA.
8
Henan Academy of Fishery Science, Zhengzhou, China.
9
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
10
Department of Psychiatry and Neurobiology Science, University of Virginia, Charlottesville, Virginia, USA.
11
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.

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.

PMID:
25240282
DOI:
10.1038/ng.3098
[Indexed for MEDLINE]

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