Generation of the first BAC-based physical map of the common carp genome
- Peng Xu†1Email author,
- Jian Wang†1,
- Jintu Wang1, 2,
- Runzi Cui1, 4,
- Yan Li1, 2,
- Zixia Zhao1,
- Peifeng Ji1,
- Yan Zhang1,
- Jiongtang Li1 and
- Xiaowen Sun1, 3Email author
© Xu et al; licensee BioMed Central Ltd. 2011
Received: 8 August 2011
Accepted: 2 November 2011
Published: 2 November 2011
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.
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/.
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.
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 . Common carp is mainly cultured in Eurasia continent with a culture history of several thousand years, and it was introduced into Africa and America some two centuries ago. In addition to its aquaculture importance, common carp is also considered as a model species for studies on ecology , environmental toxicology [3, 4], development , immunology , evolutionary genomics , nutrition , and physiology . As such, great interests exist to generate its genetic and genomic resources. Significant progress has been made recently including a large number of polymorphic genetic markers [6, 9–11], linkage maps [12, 13], a large number of ESTs (unpublished), a bacterial artificial chromosome (BAC) library , a large dataset of BAC-end sequences (BES) , and cDNA microarrays . Some of these genomic resources have been used to analyze important genes  and quantitative trait loci (QTL) related to various economic traits such as growth rate, cold-tolerance, muscle quality, and amino acid content [18, 19]. However, no physical maps have been constructed, hindering the progress of whole genome sequencing project as well as genetic improvement programs.
Common carp has a genome size of 1.6-2.0 Gb, as estimated from flow cytometry [20–22]. This is significantly larger than its closely related grass carp (1 Gb). 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 [23–25]. Such potential tetraploidization could add significant challenges to the whole genome sequencing project for common carp, a project currently in progress. Clearly, a physical map is demanded for scaffolding the small sequence contigs into scaffolds, and eventually into chromosome-scale sequence assemblies.
Physical maps have been proven as an important genome resource. A high quality physical map is very useful to understanding of genome structure and organization, and to positional cloning of genes associating to economically important traits. For genome sequencing projects, especially those using the high throughput next generation sequencing platforms, a high quality physical map and enough BAC end sequences are required to make the genome assembly accurately[26–29]. In addition, physical map could be integrated with linkage map by either mapping BAC-anchored genetic markers into linkage map or locating markers of linkage map on physical map contigs. The integrated map could be used in comparative mapping and genomic analysis of closely related species and enhance the understanding of unsequenced genomes [28, 30].
In the past decade, several physical maps have been constructed in aquaculture ray-finned fishes including Nile tilapia (Oreochromis niloticus) , Atlantic salmon (Salmo salar) , channel catfish (Ictalurus punctatus) [33, 34], rainbow trout (Oncorhynchus mykiss)  and Asian sea bass (Lates calcarifer) . Here we report the first BAC-based physical map of the common carp genome.
Results and Discussion
BAC fingerprinting and contig assembly
Statistics of the physical map assembly of the common carp
Total number of BAC clones fingerprinted
~7.3× genome equivalent
Valid fingerprints for FPC assembly
~5.9× genome coverage
Total number of contigs assembled
Clones contained in the 3696 contigs
~5.5× genome coverage
Average BAC clones per contig
Average contig size in consensus bands (CB)
Estimated average contig size (kb)
Estimated N50 contig size (kb)
Number of Q-contigs
Number of Q-clones
Number of singletons
Average insert size of the BAC library (kb)
Average number of bands per fingerprinted BAC clone
Average size each band represents (kb)
Total number of bands included in the contigs
18.2 bands per BAC clone in the consensus map
Total physical length of assembled contigs
~1× genome size
There are a total of 1,234,511 consensus bands (CB) in this assembly, representing approximate 1.76 Gb of the common carp genome (1,234,511 CB × 1.428 kb per CB). Each BAC in the contigs contributes 18.2 distinct bands or 26 kb linear length to the assembly on average. The physical length of all the assembled BAC contigs is slightly longer than our commonly used estimation (1.7 Gb) of the genome size of common carp, but shorter than the estimation of Ojima and Yamamoto . We believe that the summed length of all BAC contigs would be shorter than the real genome size as single BAC library cannot possibly cover 100% of the genome, because there would be some missing genomic regions caused by restriction enzyme bias, leaving gaps in the assembled physical map. However, a real BAC contig could be split into two contigs or more when we use assembly parameters of high stringency, especially for those genome regions with higher levels of heterozygosity.
Questionable clones (Q-clones) generally result from one or several false positive overlaps during physical map assembly. Sometimes, FPC may not be able to assign an appropriate linear order to a specific BAC clone on the consensus map, and marked it as a Q-clone. In this study, the function DQer were used to break up all contigs containing over 15% Q-clones after several rounds of end-to-end merging and single-to-end merging with lowered stringency of cutoff values progressively.
Distribution of Q-clones in assembled contigs
Number of contigs
Percentage of all contigs
The physical map of common carp is accessed through the web-based FPC viewer at http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/
Assessment of the physical map
Assessment of overlapping reliability at end to end merging points by using PCR
Clones overlapping each other
cutoff value of end merging
Assessment of assembly reliability on randomly selected contigs by using PCR with primers designed from BAC end sequences
Number of primer pairs
Number of Clones
Number of Positive Clones
Contig assembly completely validated
Validation of physical map assembly by linkage mapping of microsatellites isolated from clones in the common carp physical map.
Number of BAC Clones
Contig Length (kb)
Genetic Distance (cM)
Number of Markers
Linkage Group ID
Here we reported the construction of the first physical map of the common carp genome. The physical map was constructed with valid fingerprints of 67,493 clones (5.5 × genome coverage). The physical map can be accessed at http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/. This physical map contained 3,696 contigs with a N50 length of 688 kb. The consensus length of assembled contigs was 1.76 Gb, consistent with the estimated genome size of common carp (1.7 Gb-2.0 Gb). The assembly was validated by using PCR assays on randomly selected contigs and mapping physical map contigs on linkage map. This physical map should be useful for various genome projects of common carp, especially for the currently ongoing whole genome sequencing project of carp.
The Hin d III BAC library of common carp used for the construction of the physical map was previously reported . Briefly, the library was made from a female common carp with a total of 92,160 recombinant clones and an average insert size of 141 kb. This library represented approximately 7.6-fold genome coverage of the common carp genome.
BAC DNA isolation and fingerprinting
BAC clones were inoculated into four 96 deep-well culturing plates using a 96-pin replicator (V&P Scientific, San Diego, CA, USA). Each well of the 96 deep-well culturing plates contained 1.2 ml 2×YT medium and 12.5 μg/ml chloramphenicol. The deep-well culturing plates were then covered with air permeable seals (Excel Scientific, Victorville, CA, USA) and incubated at 37°C with 300 rpm shaking for 20 hours. BAC DNA was then isolated using a modified alkaline method with lysate clarification using Fritted Filter Plate (NUNC, Roskilde, Denmark). BAC DNA was resuspended in 50 μl of milliQ water in 96-well plates and stored at -20°C before use.
Twenty μl BAC DNA of each BAC clone was digested by Bam HI, Eco RI, Xba I, Xho I, and Hae III restriction endonucleases (New England Biolabs, Ipswich, MA, USA) at 37°C for three hours simultaneously, and then end-labeled using SNaPshot Multiplex kit (Life technologies, Foster City, CA, USA), according to manufacturer's instructions. The 6-bp cutter restriction endonucleases Eco RI (G'AATTC), Xba I (T'CTAGA), Bam HI (G'GATCC), Xho I (C'TCGAG) generate 5'-protruding ends allowing differentially fluorescence labeled A, C, G, and T to be incorporated at the 3' ends of fingerprints while the 4-bp cutter Hae III cleave the fragments to small segments making them suitable for analysis using an automated sequencer . The labeled BAC fragments were precipitated by using pre-chilled 100% ethanol following by washing with 70% ethanol, then suspended in 10 μl Hi-Di Formamide and analyzed with GeneScan 500 LIZ Size Standard on 3730XL DNA Analyzer (Life technologies).
Fingerprint collection and processing
The fragment sizes in each BAC fingerprint were collected by the Data Collection program on the ABI 3730XL Genetic Analyzer, then processed by software FPminer 2.1 . Briefly, the fragment size calling was conducted using automatic algorithm in FPminer. Several quality control steps were applied to the fingerprints: the empty wells were removed; the off-scale fragments with peak height greater than 6,000 relative fluorescent units (RFU) were removed; the fingerprints with fewer than 50 or more than 250 fragments were removed. Cross-contamination check was also conducted on FPminer to remove potential contaminated clones. In addition, the fingerprints having greater than 60 fragments of any single fluorescent color were also considered as contaminated clones and removed. Vector fragments and high frequency fragments were identified by fragment frequency analysis and then removed in FPminer. The sizes files were then output from FPminer for contig assembly in FPC program (http://www.agcol.arizona.edu/software/fpc).
The program FPC version 9.3 was used to assemble the BAC fingerprinting data into BAC contigs. FPC parameters were adjusted for the HICF method as described in the tutorials. The size tolerance was set at 0.4 bp, and Sulston score cutoff was initially set as 1e-40. After the first round of assembly, the DQer function was performed to break down all contigs more than 15% of Q clones to eliminate false assembly. Several rounds of end-to-end merging with consecutive reductions of the Sulston score cutoff stringency at 1e-15 were then performed, and followed by single-to-end merging until the final cutoff of 1e-15 was reached.
Contig quality assessment using PCR method
BAC contigs were randomly selected, and BAC-end sequences on those selected contigs were used to develop primers for contig validation and reliability examination. Briefly, all BAC clones on the selected contigs were picked from stocking plates and inoculated into culturing plates. BAC DNA was then extracted using alkaline method as we described above. PCR reactions with primers from specific contig were conducted on all BAC clones of the contig in 25 μl solution containing 10 ng BAC DNA, 1×PCR buffer, 100 μmol of each dNTPs, 0.2 μmol forward primer, 0.2 μmol reverse primer and 1 U of Taq DNA polymerase (Fermentas, Glen Burnie, Maryland, USA) on ABI 9700 thermal cycler (Life Technologies) under the following cycling conditions: initial denaturation at 95°C for 3 min; then 35 cycles of 94°C for 30 sec, 55°C for 30 sec and 72°C for 45 sec; final extension at 72°C for 5 min. All primers were listed in Additional file 1 Table S1. PCR products were then analyzed to detect positive BAC clones using electrophoresis on 1.2% agarose gel. The BAC clones that supported positive PCR amplification with a single pair of PCR primers were considered to be overlapped.
Contig validation using BAC-anchored microsatellite markers on linkage map
Microsatellite markers were previously developed from BAC end sequences and genotyped in a F1 common carp family for linkage mapping (Zhang et al, unpublished). The linkage map contained 271 BAC-derived microsatellite markers, which could serve anchor points for physical and linkage map integration. Physical map contigs containing at least one anchor microsatellite markers were then mapped to linkage map. The contigs harboring two or more BAC-anchored microsatellite markers were collected for assembly assessment. Microsatellite markers on one physical map contig should be also mapped to one linkage group with reasonable genetic distance if physical map was assembled correctly.
This study was supported by the grants from National Department Public Benefit Research Foundation (No. 200903045), National High-tech R&D Program of China (No. 2009AA10Z105 and 2011AA100401), China Ministry of Agriculture "948" Program (No. 2010-Z11) and Research Foundation of Chinese Academy of Fishery Sciences (No. 2009B002).
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