ArticleGenome biology2010
Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 2 of them syntheses that pooled it.
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Who cites it
42 citing papers in PubMed, 2 syntheses or guidelines pooled it, 96 citations in OpenAlex.
- A Systematic Review of Hospital-to-School Reintegration Interventions for Children and Youth with Acquired Brain Injury.PloS one · 2015Pooled it
- The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets.Biochimica et biophysica acta · 2014Pooled it
- Article
- Environment-Dependent Heterosis and Transgressive Gene Expression in Reciprocal Hybrids between the Channel CatfishBiology · 2022Article
- Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function.Frontiers in microbiology · 2018Article
- Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence.Scientific reports · 2017Article
- The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.Nature communications · 2016Article
- Testing the evolutionary conservation of vocal motoneurons in vertebrates.Respiratory physiology & neurobiology · 2016Article
- Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.Molecular biology and evolution · 2016Article
- Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish.BMC genomics · 2015Article
- Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.PloS one · 2015Article
- A candidate gene association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii ) culture line.Marine biotechnology (New York, N.Y.) · 2014Article
- Development of the catfish 250K SNP array for genome-wide association studies.BMC research notes · 2014Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays.International journal of molecular sciences · 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
- Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates.Molecular biology and evolution · 2013Article
- Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes.Marine biotechnology (New York, N.Y.) · 2013Article
- Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.PloS one · 2013Article
- Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii.PloS one · 2013Article
Corrections and comments
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Authors and funding
42 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThrough the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification.
resultsA total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis.
conclusionsThis project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.
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