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United States Department of Agriculture

Agricultural Research Service

Title: Characterization of a BAC Library from Channel Catfish Ictalurus punctatus: Indications of High Rates of Evolution Among Teleost Genomes

item Wang, S
item Xu, P
item Thorsen, J
item Zhu, B
item De Jong, P
item Waldbieser, Geoffrey - Geoff
item Kucuktas, H
item Liu, Z

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2007
Publication Date: 12/1/2007
Citation: Wang, S., Xu, P., Thorsen, J., Zhu, B., De Jong, P.J., Waldbieser, G.C., Kucuktas, H., Liu, Z. 2007. Characterization of a BAC Library from Channel Catfish Ictalurus punctatus: Indications of High Rates of Evolution Among Teleost Genomes. Marine Biotechnology 9:701-711.

Interpretive Summary: Catfish genetic improvement depends on the identification of chromosomal regions, and eventually gene sequences, controlling important production traits. However, resources useful for identification of these sequences have been limited. Therefore a genomic DNA library was produced using genomic DNA from a single male catfish. On average, each DNA clone in the library contained a 161,000 base pair segment of the 1 billion base pair catfish genome. This research also produced 20,00 partial DNA sequences from the ends of these clones. Further analysis of sequences from both ends of the same DNA clone showed only 24% of the ends were conserved in the zebrafish or pufferfish genomes. The low conservation of DNA sequence at 160,000 base pair lengths suggested a high level of intrachromosomal rearrangements between these species. These results point to the need for extensive sequencing of the catfish genome in order to utilize comparative genomic approaches to identification of chromosomal regions controlling production traits.

Technical Abstract: The CHORI-212 bacterial artificial chromosome (BAC) library was constructed by cloning EcoRI/EcoRI partially digested DNA into the pTARBAC2.1 vector. The library has an average insert size of 161 kb, and provides 10.6-fold coverage of the channel catfish haploid genome. Screening of 32 genes using overgo or cDNA probes indicated that this library had a good representation of the genome as all tested genes existed in the library. We previously reported sequencing of approximately 25,000 BAC ends that generated 20,366 high-quality BAC end sequences (BES) and identified a large number of sequences similar to known genes using BLASTX searches. In this work, particular attention was given to identification of BAC mate pairs with known genes from both ends. When identified, comparative genome analysis was conducted to determine syntenic regions of the catfish genome with the genomes of zebrafish and Tetraodon. Of the 141 mate pairs with known genes from channel catfish, conserved syntenies were identified in 34 (24.1%), with 30 conserved in the zebrafish genome and 14 conserved in the Tetraodon genome. Additional analysis of three of the 34 conserved syntenic groups by direct sequencing indicated conserved gene contents in all three species. This indicates that comparative genome analysis may provide shortcuts to genome analysis in catfish, especially for short genomic regions once the conserved syntenies are identified.

Last Modified: 10/17/2017
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