title: Genome sequence and genetic diversity of the common carp, Cyprinus carpio.
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.
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xumin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jiongtang
authors.initials: J
authors.lastname: Li
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guiming
authors.initials: G
authors.lastname: Liu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Youyi
authors.initials: Y
authors.lastname: Kuang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Xianhu
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Lufeng
authors.initials: L
authors.lastname: Ren
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guoliang
authors.initials: G
authors.lastname: Wang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Linhe
authors.initials: L
authors.lastname: Huo
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Zixia
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Dingchen
authors.initials: D
authors.lastname: Cao
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Cuiyun
authors.initials: C
authors.lastname: Lu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: Stem Cell Program, Division of Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: 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.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Fan
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guangle
authors.initials: G
authors.lastname: Shan
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xingang
authors.initials: X
authors.lastname: Li
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Shuangxiu
authors.initials: S
authors.lastname: Wu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Lipu
authors.initials: L
authors.lastname: Song
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Guangyuan
authors.initials: G
authors.lastname: Hou
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Research Institute for Fisheries, Aquaculture and Irrigation, Szarvas, Hungary.
authors.forename: Zsigmond
authors.initials: Z
authors.lastname: Jeney
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Yu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Changjun
authors.initials: C
authors.lastname: Shao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Lai
authors.initials: L
authors.lastname: Song
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Sun
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Peifeng
authors.initials: P
authors.lastname: Ji
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Liming
authors.initials: L
authors.lastname: Xu
authors.affiliation: Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, USA.
authors.forename: Fanyue
authors.initials: F
authors.lastname: Sun
authors.affiliation: Henan Academy of Fishery Science, Zhengzhou, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Feng
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
authors.forename: Chenghui
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Psychiatry and Neurobiology Science, University of Virginia, Charlottesville, Virginia, USA.
authors.forename: Shaolin
authors.initials: S
authors.lastname: Wang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Baosen
authors.initials: B
authors.lastname: Wang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xue
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jintu
authors.initials: J
authors.lastname: Wang
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Weihua
authors.initials: W
authors.lastname: Lv
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Kejing
authors.initials: K
authors.lastname: Wu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jiayan
authors.initials: J
authors.lastname: Wu
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: 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.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
mesh_terms: D000818:Animals; D001483:Base Sequence; D002347:Carps / Q000235:genetics*; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D040481:Genome Components / Q000235:genetics; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D012867:Skin / Q000378:metabolism; D013045:Species Specificity