Open Access Highly Accessed Research article

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

Peng Xu1*, Jian Wang1, Jintu Wang12, Runzi Cui14, Yan Li12, Zixia Zhao1, Peifeng Ji1, Yan Zhang1, Jiongtang Li1 and Xiaowen Sun13*

Author Affiliations

1 The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China

2 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

3 Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China

4 College of Life Science, Tianjin Normal University, Tianjin, 300387, China

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BMC Genomics 2011, 12:537  doi:10.1186/1471-2164-12-537

Published: 2 November 2011

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/ webcite.

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.