ArticleBMC genomics2013
Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing.Scientific reports · 2017Article
- BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome.Scientific reports · 2016Article
- Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.Molecular biology and evolution · 2016Article
- Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth.Scientific reports · 2015Article
- Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- 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
- A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome.BMC genomics · 2014Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.PloS one · 2013Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative 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 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.
resultsWith 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. Large numbers 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. Of the 287 genes, 35 genes were found to be duplicated in the catfish genome, with the vast majority of the duplications being interchromosomal.
conclusionsComparative genome analysis is a powerful tool even in the absence of a well-assembled whole 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 are 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.
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