Correlation Engine 2.0
Clear Search sequence regions


  • 3 utr (1)
  • actin (1)
  • alaska (1)
  • alcohol dependence (1)
  • aldehyde (3)
  • aldh9a1a (3)
  • alleles (16)
  • ammonia (8)
  • and viruses (1)
  • asian (1)
  • behaviours (2)
  • blue (12)
  • blue colour (2)
  • bodies water (5)
  • brain (8)
  • bright red (1)
  • british columbia (7)
  • bwa (3)
  • CACNA1G (8)
  • calc (2)
  • calcium channel (7)
  • canada (3)
  • case (4)
  • central nervous system (1)
  • cGMP (2)
  • chromatin (1)
  • chromium (3)
  • chromosomes d (1)
  • chromosomes groups (2)
  • complement c3 (4)
  • control positives (1)
  • cpa6 (5)
  • data file (12)
  • dcps (1)
  • dna damage (1)
  • dna fragments (1)
  • dna libraries (5)
  • dna repair (1)
  • duplicates (1)
  • electrophoresis (1)
  • elements (3)
  • Eric (1)
  • esox (4)
  • essential (1)
  • ethanol (1)
  • factor (20)
  • fiber (1)
  • FKBP6 (3)
  • Forkhead (1)
  • fresh water (2)
  • Gbp (4)
  • genbank (3)
  • gene cluster (4)
  • genes (40)
  • genomes (4)
  • genotypes (14)
  • GREB1- like protein (5)
  • green colour (1)
  • haploid (4)
  • heart (1)
  • help (3)
  • human (4)
  • human activities (1)
  • immunoglobulin (2)
  • immunoglobulin chain (9)
  • immunoglobulin gene (1)
  • isoforms (2)
  • japan (1)
  • k 10 (1)
  • knockout mice (1)
  • l- type calcium channels (1)
  • LIN28B (6)
  • liver (1)
  • LOC115106380 (2)
  • maf (3)
  • mammals (1)
  • mate (7)
  • max1 (1)
  • Mbp (19)
  • mem (3)
  • metrics (3)
  • MHC class II (1)
  • mice (4)
  • minal (1)
  • minor (1)
  • mrna (2)
  • mtdna (1)
  • Mtr4 (5)
  • new england (4)
  • north america (1)
  • northwest territories (1)
  • NRG3 (5)
  • nucleotides (1)
  • ocean (12)
  • oncorhynchus (1)
  • oncorhynchus kisutch (10)
  • oncorhynchus nerka (7)
  • oncorhynchus tshawytscha (1)
  • ovaries (1)
  • paralogs (2)
  • parr (2)
  • PDE6C (2)
  • phenotypes (2)
  • picogreen (2)
  • plexin A2 (3)
  • prepares (1)
  • protein- genes (7)
  • python (3)
  • RAD (7)
  • rainbow trout (3)
  • reads (24)
  • reagents (2)
  • region rich (1)
  • research (4)
  • retina (4)
  • RGS6 (4)
  • rna (21)
  • rna sequence (1)
  • russia (1)
  • salmo salar (3)
  • salmonid (10)
  • sarcoglycan (2)
  • sarcoglycan- complex (3)
  • sarcospan (4)
  • sdY (17)
  • sed (1)
  • segment (8)
  • sex chromosomes (12)
  • SGCD (3)
  • signals (3)
  • six homeobox 6 (2)
  • SMARCAL1 (1)
  • SMRT (2)
  • SNP (10)
  • sperm (9)
  • spermatid (1)
  • spermatogonia (1)
  • spleen (1)
  • sspn (2)
  • stem cell (2)
  • stomach (1)
  • t type calcium channel (1)
  • TIF (7)
  • TLN2 (6)
  • trout (2)
  • v1 9 (3)
  • VCF (8)
  • vtcn1 (1)
  • y chromosome (6)
  • zebrafish (2)
  • Sizes of these terms reflect their relevance to your search.

    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.

    Citation

    Kris A Christensen, Eric B Rondeau, David R Minkley, Dionne Sakhrani, Carlo A Biagi, Anne-Marie Flores, Ruth E Withler, Scott A Pavey, Terry D Beacham, Theresa Godin, Eric B Taylor, Michael A Russello, Robert H Devlin, Ben F Koop. The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PloS one. 2020 Oct 29;15(10):e0240935

    Expand section icon Mesh Tags

    Expand section icon Substances


    PMID: 33119641

    View Full Text