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Nature genetics:Genome sequence and genetic diversity of the common carp, Cyprinus carpio  

2014-09-22 08:44:17|  分类: 文献学习 |  标签: |举报 |字号 订阅

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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.

Nature genetics:Genome sequence and genetic diversity of the common carp, Cyprinus carpio - 喜欢吃桃子 - wangyufeng的博客
(a) A maximum-likelihood phylogenetic tree of ten strains of common carp generated on the basis of SNPs. Strain abbreviations: Sp, Songpu; D, Danube; Sz, Szarvas; NA, North American; Y, Yellow River; H, Heilongjiang; O, Oujiang color; Hb, Hebao; X, Xingguo; K, koi. (b) PCA of C. carpio strains. (c) The population structure of common carp strains. Each color represents one ancestral population; each strain is represented by a vertical bar, and the length of each colored segment in each vertical bar represents the proportion contributed by ancestral populations. K = 3 and 4 was used for analysis with the highest ln value.

Primary accessions

BioProject

European Nucleotide Archive

Referenced accessions

Sequence Read Archive

Fulltext:http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3098.html#author-information



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