ArticleBMC genomics2008
A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 195 citations in OpenAlex.
- Review
- New Insights Into the Evolution of Corticotropin-Releasing Hormone Family With a Special Focus on Teleosts.Frontiers in endocrinology · 2022Article
- Molecular Phylogeny and Adaptive Mitochondrial DNA Evolution of Salmonids (Pisces: Salmonidae).Frontiers in genetics · 2022Article
- Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array.Animals : an open access journal from MDPI · 2021Article
- AFrontiers in genetics · 2021Article
- The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.PloS one · 2020Article
- A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication.G3 (Bethesda, Md.) · 2018Article
- De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species.BMC genomics · 2018Article
- Article
- Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs.PeerJ · 2018Article
- Article
- Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C).BMC genomics · 2015Article
- Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system.BMC genomics · 2015Article
- Identification and de novo sequencing of housekeeping genes appropriate for gene expression analyses in farmed maraena whitefish (Coregonus maraena) during crowding stress.Fish physiology and biochemistry · 2015Article
- Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.PloS one · 2015Article
- Transcriptomic responses of Atlantic salmon (Salmo salar) to environmental enrichment during juvenile rearing.PloS one · 2015Article
- Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive life span.Ecology and evolution · 2014Article
- Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon.Genome biology and evolution · 2014Article
- Heritable targeted inactivation of the rainbow trout (Oncorhynchus mykiss) master sex-determining gene using zinc-finger nucleases.Marine biotechnology (New York, N.Y.) · 2014Article
- Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis.BMC genomics · 2014Article
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Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSalmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish.
results298,304 expressed sequence tags (ESTs) from Atlantic salmon (69% of the total), 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species.
conclusionAn extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94-96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is consistent with an ancestral salmonid genome duplication hypothesis. Genome resources, including a new 32 K microarray, provide valuable new tools to study salmonids.
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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.