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

Peng Xu,Zixia Zhao,Runzi Cui,Jintu Wang,Yan Zhang,Yan Li,Jiongtang Li,Peifeng Ji,Jian Wang,Xiaowen Sun

doi:10.1186/1471-2164-12-537

Peng Xu, Zixia Zhao + Show 8 more

Open Access

https://doi.org/10.1186/1471-2164-12-537

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Abstract

BackgroundCommon 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.ResultThe 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/.ConclusionThe 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.

Highlights

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
A total of 89,088 bacterial artificial chromosome (BAC) clones, representing around 7.3-fold coverage of the common carp genome, were processed. Of these processed BAC clones, a total of 72,158 (81% success) fingerprints were used for the construction of the physical map after removal of low quality fingerprints using FPminer 2.1 [38]
The results showed that PCR can successfully amplify positive products on the junctions of eight selected contigs, indicating that both BAC clones on the junction site were truly overlapped in the common carp genome (Table 3)

Summary

Introduction

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. In spite of much progress, no physical maps have been available for common carp. Along with its large genome size, common carp has twice as many chromosomes as most other cyprinid fishes, making many to believe that an additional round of whole genome duplication (4R) may have occurred 50 Myr ago [23,24,25]. Such potential tetraploidization could add significant challenges to the whole genome sequencing project for common carp, a project currently in progress. A physical map is demanded for scaffolding the small sequence contigs into scaffolds, and eventually into chromosome-scale sequence assemblies

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