Complete Sequence and Characterization of the Channel Catfish Mitochondrial Genome

Abstract

In order to support analysis of channel catfish populations and genetic improvement programs, the channel catfish, Ictalurus punctatus, mitochondrial genome was completely sequenced and revealed gene structure and gene order common to vertebrates. Nucleotide sequence comparisons of cytochrome b (Cytb) and cytochrome c oxidase subunit 1 (COI) demonstrated genetic separation of the genera Ictalurus, Pylodictis and Ameiurus consistent with the taxonomic classification within Ictaluridae. The ictalurid Cytb nucleotide sequences were significantly different from a putative channel catfish Cytb sequence in GenBank. Genetic relationships based on mitochondrial DNA sequences indicated the value of channel catfish in genomic comparisons between teleosts. Pairwise alignment of DNA sequences revealed conservation of regulatory sequences in the D-loop region with other vertebrates. Analysis of D-loop sequences in commercial populations and a research strain revealed 28 polymorphic sites and 33 D-loop haplotypes. Sequence analysis revealed clustering of haplotypes within commercial farms and the USDA103 research line, but D-loop haplotypes were not sufficient to discriminate the USDA103 fish from commercial catfish.

Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration

“…The analysis reflected the observed vertebrate bias against G on the L-strand. The A + T content was 51.9%, a similar value to that determined for other bony fishes (Tzeng et al, 1992;Waldbieser et al, 2003;Wang et al, 2007).…”

Diversification of Sisorid catfishes (Teleostei: Siluriformes) in relation to the orogeny of the Himalayan Plateau

“…Multiple sequence alignment was performed using MegAlign. All protein-coding, rRNA and tRNA genes were identified by comparison with known sequences from other catfish taxa, such as Ictalurus punctatus [25], Cranoglanis bouderius [26], Pseudobagrus tokiensis [27] and Pangasianodon gigas [28]. All tRNA genes were confirmed with tRNAscan-SE Search Server available online (http://lowelab.ucsc.edu/tRNAscan-SE/).…”

A review of catfish genomics: progress and perspectives

“…At least 35 mitochondrial haplotypes have been identified in catfish populations. The sequence and polymorphic information should be useful for parentage analysis and strain analysis in catfish [36].…”