A BAC-based physical map of the channel catfish genome

Peng Xu, Shaolin Wang, Lei Liu, Jim Thorsen, Huseyin Kucuktas, Zhanjian "John" Liu

Research output: Contribution to journalArticle

60 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 languageEnglish (US)
Pages (from-to)380-388
Number of pages9
JournalGenomics
Volume90
Issue number3
DOIs
StatePublished - Sep 2007
Externally publishedYes

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Keywords

  • BAC
  • Catfish
  • Contig
  • Fingerprint
  • Genome
  • Physical map

ASJC Scopus subject areas

  • Genetics

Cite this

Xu, P., Wang, S., Liu, L., Thorsen, J., Kucuktas, H., & Liu, Z. J. (2007). A BAC-based physical map of the channel catfish genome. Genomics, 90(3), 380-388. https://doi.org/10.1016/j.ygeno.2007.05.008