ArticlePloS one2020
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.Molecular ecology · 2025Review
- Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.BMC genomics · 2025Article
- Application of Genomic Offsets to Inform Freshwater Fisheries Management Under Climate Change.Evolutionary applications · 2025Article
- Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.BMC genomics · 2025Review
- Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly.G3 (Bethesda, Md.) · 2025Article
- Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms.Molecular ecology · 2024Article
- Article
- Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.G3 (Bethesda, Md.) · 2024Article
- Genomic vulnerability of a freshwater salmonid under climate change.Evolutionary applications · 2024Article
- A study on the codon usage bias of arenavirus common genes.Frontiers in microbiology · 2024Article
- The late-evolving salmon and trout join the GnRH1 club.Histochemistry and cell biology · 2023Article
- Allele surfing causes maladaptation in a Pacific salmon of conservation concern.PLoS genetics · 2023Article
- Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.G3 (Bethesda, Md.) · 2023Article
- Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome.G3 (Bethesda, Md.) · 2023Article
- A homology guide for Pacific salmon genusEcology and evolution · 2023Article
- A chromosome-level genome of Brachymystax tsinlingensis provides resources and insights into salmonids evolution.G3 (Bethesda, Md.) · 2022Article
- An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly.G3 (Bethesda, Md.) · 2022Article
- Genome-wide analysis reveals demographic and life-history patterns associated with habitat modification in landlocked, deep-spawning sockeye salmon (Ecology and evolution · 2021Article
- Correction: The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.PloS one · 2021Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes-the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.