Towards the Complete Genome: Progress of Common Carp Genome Project

Common carp is one of the most important aquaculture species in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. Common carp is tetroploid teleost fish with an estimated haploid genome size of about 1700 Mbp and 2n = 100 chromosomes. Although molecular genetics study of common carp had been conducted productively in China for breeding and genetic improvement purpose, genomic resources of the common carp are still relatively underdeveloped until the Common Carp Genome Project (CCGP) was initiated on December 2009. The project aims at building the necessary tools and resources, identifying commercial important genes or traits and boosting the aquaculture industry of common carp. Besides, CCGP will also provide valuable genome data for the study of vertebrate genome evolution and phylogeny as common carp may involve an additional 4^th Round of Whole Genome Duplication. CCGP currently includes following tasks: whole genome shotgun deep sequencing and draft assembly employing the next generation sequencing technology, BAC library construction and genome-wide BAC-end sequencing, BAC-based physical mapping, genome-wide marker development and high-density linkage mapping, FISH-based chromosome mapping, transcriptome deep sequencing and genome annotation, functional genomics, bioinformatics and database construction. To date, whole genome sequencing had been completed using multiple platforms including Roche 454, Illumina, SOLiD and traditional Sanger method with various library insertion lengths, generating 175 folds of common carp genome equivalence. The assembled genome has scaffold N50 length of 1.14 Mb and contig N50 length of 31 .1 kb, covering 1710 Mb of common carp. Transcriptome sequences had been collected from both Roche 454 and Illumina HiSeq 2000 platforms. Genome annotation was performed based on transcriptome homology and de novo prediction methods. A total of 31404 genes was annotated in the genome with average length 1917 bp. The fingerprint from over 90,000 BACs of 7x genome equivalence had been collected and the first BAC-based physical map of common carp was constructed, containing 3696 BAC contigs with the N50 length of 688 kb. Over 800,000 SNPs and 13,000 microsatellite loci had been identified from common carp cDNA and BAC-end sequences for high density linkage mapping and map integration. The high-density linkage map of common carp had been constructed with approximate 6000 markers, including around 5000 SNP markers and 1000 SSR markers. The completion of CCGP will lead to better management of breeding selection, disease prevention and transgenic study on the common carp, as well as the other Cyprinidae species.