Correction: The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
| Autor: | Kris A. Christensen, David R. Minkley, Michael A. Russello, Dionne Sakhrani, Carlo A. Biagi, Eric Rondeau, Theresa Godin, Terry D. Beacham, Eric B. Taylor, Scott A. Pavey, Anne-Marie Flores, Ruth E. Withler, Ben F. Koop, Robert H. Devlin |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Candidate gene Heredity Sequence assembly 01 natural sciences Genome Homozygosity Salmon education.field_of_study Heterozygosity Multidisciplinary Ecotype High-Throughput Nucleotide Sequencing Eukaryota Genomics Osteichthyes Vertebrates Oncorhynchus Medicine Immunoglobulin Heavy Chains Research Article Fish Proteins Science Population Biology 010603 evolutionary biology Chromosomes 03 medical and health sciences Fish Genomics Genetics Animals education Alleles Fish migration Whole Genome Sequencing Sequence Analysis RNA Gene Expression Profiling Organisms Correction Genetic Variation Biology and Life Sciences biology.organism_classification 030104 developmental biology Fish Evolutionary biology Animal Genomics Genetic Loci Zoology |
| Zdroj: | PLoS ONE, Vol 15, Iss 10, p e0240935 (2020) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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