Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio

Abstract

A bacterial artificial chromosome (BAC) library of common carp Cyprinus carpio L. was constructed as a part of ongoing common carp genome project, which is aiming assembly of common carp genome. The library, containing a total of 92,160 BAC clones with an average insert size of 141 kb, was constructed into the restriction site of Hind III on BAC vector CopyControl pCC1BAC, covering 7.7 X haploid genome equivalents. Three dimension pools and superpools of the BAC library were established and 23 positive clones of 14 targets were identified from one-fifth of the BAC library. Pilot project of BAC end sequencing was conducted on 2,688 BAC ends from 1,344 clones and harvested 2,522 high-quality Q20 sequences with average length of 677 bp. The sequencing success rate was 93.8% and pair-end success rate was 92.3%. A total of 212 microsyntenies had been established between common carp and zebrafish genomes as a trial for genome-wide comparative genomics in these two closely related species.