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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetics, Physiology, and Health Research to Improve Catfish Production

Location: Warmwater Aquaculture Research Unit

Title: Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements

Authors
item Zhang, Yu -
item Liu, Shikai -
item Lu, Jianguo -
item Jiang, Yanliang -
item Sungao, Xiaoyu -
item Ninwichian, Parichart -
item Li, Chao -
item Waldbieser, Geoffrey
item Liu, Zhanjiang -

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 16, 2013
Publication Date: June 10, 2013
Citation: Zhang, Y., Liu, S., Lu, J., Jiang, Y., Sungao, X., Ninwichian, P., Li, C., Waldbieser, G.C., Liu, Z. 2013. Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements. Biomed Central (BMC) Genomics. 14:387.

Interpretive Summary: At present, the co-linear relationships between genomic DNA sequences contigs of catfish and other bony fish genomes are unknown. A pilot study involving scientists at Auburn University and the USDA, ARS, Catfish Genetics Research Unit compared next-generation DNA sequence contigs from a catfish linkage group with sequences from genome assemblies of other bony fishes. The analysis revealed significant structural similarities between catfish and other model fish species but also revealed extensive inter- and intra-chromosomal rearrangements between the species. This information will facilitate the annotation of the catfish genome, and scientists can infer structural and functional relationships of catfish genes based on knowledge available from other fish genomes.

Technical Abstract: Background Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a powerful platform for comparative genomic analysis between catfish and other model teleost fish species. This study aimed to gain understanding of genome organizations and similarities among catfish and several sequenced teleost genomes using linkage group 8 (LG8) as a pilot study. Results With existing genome resources, 287 unique genes were identified in LG8. Comparative genome analysis indicated that most of these 287 genes on catfish LG8 are located on two homologous chromosomes of zebrafish, medaka, stickleback, and three chromosomes of green-spotted pufferfish. A large number of conserved syntenies were identified. Detailed analysis of the conserved syntenies in relation to chromosome level similarities revealed extensive inter-chromosomal and intra-chromosomal rearrangements during evolution. A set of potentially duplicated genes were identified which could provide the foundation for whole genome sequence assembly and annotation. Conclusions Comparative genome analysis is a powerful tool even in the absence of a well-assembled genome sequence. In spite of sequence stacking due to low resolution of the linkage and physical maps, conserved syntenies can be identified although the exact gene order and orientation is unknown at present. Through chromosome-level comparative analysis, homologous chromosomes among teleosts can be identified. Syntenic analysis should facilitate annotation of the catfish genome, which in turn, should facilitate functional inference of genes based on their orthology.

Last Modified: 7/28/2014
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