ArticleBMC genomics2009
Comparative analysis of catfish BAC end sequences with the zebrafish genome.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- BAC-FISH Based Physical Map of Endangered CatfishInternational journal of molecular sciences · 2022Article
- Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts.Marine biotechnology (New York, N.Y.) · 2019Article
- A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.BMC genomics · 2018Article
- The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.Nature communications · 2016Article
- Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata.BMC research notes · 2014Article
- Development of the catfish 250K SNP array for genome-wide association studies.BMC research notes · 2014Article
- Generation of physical map contig-specific sequences.Frontiers in genetics · 2014Review
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements.BMC genomics · 2013Article
- A consensus linkage map provides insights on genome character and evolution in common carp (Cyprinus carpio L.).Marine biotechnology (New York, N.Y.) · 2013Article
- A dense genetic linkage map for common carp and its integration with a BAC-based physical map.PloS one · 2013Article
- Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.PloS one · 2013Article
- Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map.G3 (Bethesda, Md.) · 2012Article
- A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.Marine biotechnology (New York, N.Y.) · 2012Article
- Article
- Generation of the first BAC-based physical map of the common carp genome.BMC genomics · 2011Article
- Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio.Marine biotechnology (New York, N.Y.) · 2011Article
- Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences.BMC genomics · 2011Article
- The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish.
resultsWe reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3%) had significant BLAST hits to the zebrafish genome (cutoff value <or= e(-5)), of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds.
conclusionBAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.
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