Generation of the first BAC-based physical map of the common carp genome

Abstract

Background: Common carp (Cyprinus carpio), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits. In spite of much progress, no physical maps have been available for common carp. The objective of this project was to generate a BAC-based physical map using fluorescent restriction fingerprinting.

Result: The first generation of common carp physical map was constructed using four- color High Information Content Fingerprinting (HICF). A total of 72,158 BAC clones were analyzed that generated 67,493 valid fingerprints (5.5 × genome coverage). These BAC clones were assembled into 3,696 contigs with the average length of 476 kb and a N50 length of 688 kb, representing approximately 1.76 Gb of the common carp genome. The largest contig contained 171 BAC clones with the physical length of 3.12 Mb. There are 761 contigs longer than the N50, and these contigs should be the most useful resource for future integrations with linkage map and whole genome sequence assembly. The common carp physical map is available at http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/.

Conclusion: The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits.

Figure 1

Bands distribution in BAC fingerprints of the common carp.

Figure 2

Distribution of BAC clones in contigs.

Figure 3

Example of common carp contig anchored to a genetic linkage group using microsatellites isolated from BAC end sequences. The contig 251, containing 55 BAC clones, has two microsatellite markers (CAFS1533 and CAFS2305) mapped to linkage group 11. The linkage distance between CAFS1533 and CAFS2305 is 0.8 cM.