A BAC-based physical map of the channel catfish genome

Peng Xu; Shaolin Wang; Lei Liu; Jim Thorsen; Huseyin Kucuktas; Zhanjiang Liu

doi:10.1016/j.ygeno.2007.05.008

A BAC-based physical map of the channel catfish genome

Peng Xu, Shaolin Wang, Lei Liu, Jim Thorsen, Huseyin Kucuktas, Zhanjiang Liu

Research output: Contribution to journal › Article › peer-review

65 Scopus citations

Abstract

Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6× genome coverage) were generated for the FPC assembly of the BAC contigs. A total of 3307 contigs were assembled using a cutoff value of 1 × 10^-20. Each contig contains an average of 9.25 clones with an average size of 292 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of the channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly and validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits.

Original language	English (US)
Pages (from-to)	380-388
Number of pages	9
Journal	Genomics
Volume	90
Issue number	3
DOIs	https://doi.org/10.1016/j.ygeno.2007.05.008
State	Published - Sep 2007
Externally published	Yes

Keywords

BAC
Catfish
Contig
Fingerprint
Genome
Physical map

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2007.05.008

Cite this

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title = "A BAC-based physical map of the channel catfish genome",

abstract = "Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6× genome coverage) were generated for the FPC assembly of the BAC contigs. A total of 3307 contigs were assembled using a cutoff value of 1 × 10-20. Each contig contains an average of 9.25 clones with an average size of 292 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of the channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly and validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits.",

keywords = "BAC, Catfish, Contig, Fingerprint, Genome, Physical map",

author = "Peng Xu and Shaolin Wang and Lei Liu and Jim Thorsen and Huseyin Kucuktas and Zhanjiang Liu",

note = "Funding Information: This project was supported by a grant from the USDA NRI Animal Genome Tools and Resources Program (Award 2006-35616-16685). We are grateful for an equipment grant from the National Research Initiative Competitive (Grant 2005-35206-15274) from the USDA Cooperative State Research, Education, and Extension Service. We thank Dr. Pieter de Jong at the Children{\textquoteright}s Hospital of the Oakland Research Institute for providing us with the CHORI-212 channel catfish BAC library. We are very grateful to Dr. Ryan Kim and Chris Wright of the University of Illinois for electrophoresis runs of the fingerprints on their ABI Prism 3730 DNA sequencers. ",

year = "2007",

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doi = "10.1016/j.ygeno.2007.05.008",

language = "English (US)",

volume = "90",

pages = "380--388",

journal = "Genomics",

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publisher = "Academic Press Inc.",

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AU - Xu, Peng

AU - Wang, Shaolin

AU - Liu, Lei

AU - Thorsen, Jim

AU - Kucuktas, Huseyin

AU - Liu, Zhanjiang

N1 - Funding Information: This project was supported by a grant from the USDA NRI Animal Genome Tools and Resources Program (Award 2006-35616-16685). We are grateful for an equipment grant from the National Research Initiative Competitive (Grant 2005-35206-15274) from the USDA Cooperative State Research, Education, and Extension Service. We thank Dr. Pieter de Jong at the Children’s Hospital of the Oakland Research Institute for providing us with the CHORI-212 channel catfish BAC library. We are very grateful to Dr. Ryan Kim and Chris Wright of the University of Illinois for electrophoresis runs of the fingerprints on their ABI Prism 3730 DNA sequencers.

PY - 2007/9

Y1 - 2007/9

N2 - Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6× genome coverage) were generated for the FPC assembly of the BAC contigs. A total of 3307 contigs were assembled using a cutoff value of 1 × 10-20. Each contig contains an average of 9.25 clones with an average size of 292 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of the channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly and validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits.

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KW - BAC

KW - Catfish

KW - Contig

KW - Fingerprint

KW - Genome

KW - Physical map

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A BAC-based physical map of the channel catfish genome

Abstract

Keywords

ASJC Scopus subject areas

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