ArticleMarine biotechnology (New York, N.Y.)2012
A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.
Article in Marine biotechnology (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes.Communications biology · 2024Article
- Review
- Review
- Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout.G3 (Bethesda, Md.) · 2020Article
- Genome-Wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout (G3 (Bethesda, Md.) · 2019Article
- At Least Two Genes Encode Many Variants of Irak3 in Rainbow Trout, but Neither the Full-Length Factor Nor Its Variants Interfere Directly With the TLR-Mediated Stimulation of Inflammation.Frontiers in immunology · 2019Article
- Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array.PloS one · 2018Article
- Article
- Identification of single-nucleotide polymorphism markers associated with cortisol response to crowding in rainbow trout.Marine biotechnology (New York, N.Y.) · 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
- Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout.Frontiers in genetics · 2015Article
- Article
- Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.PloS one · 2015Article
- A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.G3 (Bethesda, Md.) · 2014Article
- Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss).Marine biotechnology (New York, N.Y.) · 2014Article
- Detection of QTL in rainbow trout affecting survival when challenged with Flavobacterium psychrophilum.Marine biotechnology (New York, N.Y.) · 2014Article
- The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.Nature communications · 2014Article
- Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing.Evolutionary applications · 2014Article
- Genetics and genomics of disease resistance in salmonid species.Frontiers in genetics · 2014Review
- Comparative genome mapping between Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (O. mykiss) based on homologous microsatellite loci.G3 (Bethesda, Md.) · 2013Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.