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Oncorhynchus mykiss gairdneri strain:Keithly Creek | breed:Interior Columbia Basin; Snake River drainage | cultivar:Redband Trout Genome sequencing and assembly

dataset
posted on 2024-06-11, 05:07 authored by US Department of Agriculture
Currently, we are working towards generating a rainbow trout pan-genome reference that will better represent the genetic diversity in this species using de-novo chromosome level assemblies. To that end we have previously generated the reference genome from the Arlee line (USDA_OmykA_1.1; GCA_013265735.3), an improved assembly for the Swanson line (Omyk_2.0; GCA_025558465.1), and a genome assembly from the Whale Rock Male line (USDA_OmyWR_1.0; GCA_029834435.1). The Swanson YY male line was originated from a semi-domesticated resident fish from the Kenai Peninsula in Alaska with a haploid number of 29 chromosomes. The Arlee doubled haploid YY male line has a different genetic background from the Swanson line. It was originated from a well-known domesticated hatchery strain that was originally collected from the northern California coast. It has a haploid number of 32 chromosomes. The three Swanson chromosomes that are being divided to two acrocentric chromosomes are Omy04, 14 and 25. The Whale Rock line is also a YY male. Like the Arlee line, it has 2N=64 chromosomes and it was originated from the Central California Coast. The one known major difference is that it was originated from a wild fish from a landlocked steelhead population. The current de-novo chromosome level assembly is from a Keithley Creek (KC) male rainbow trout. The KC is from the inland lineage of rainbow trout (O. m. gairdneri) in contrast to the three previous assemblies that were done using fish from the coastal lineage (O. m. irideus). It is also known as Redband trout, with geographic distribution from the Interior Columbia Basin; Snake River Drainage. Life history is resident, and it is an offspring of fish collected from the wild, thus representing a wild population. The KC population of Redband trout is from the Montane ecosystem in contrast with the desert Redband trout. The exact Karyotype of the KC population is unknown. Our de-novo chromosome level genome assembly provides strong support for 2N=60 number of chromosomes. The sex determination gene (sdY) is located on Chromosome 29.

Funding

U.S. Department of Agriculture, 8082-31000-013-00D

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2023-12-20

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

genomics; sequence analysis; genome

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA1027447

Preferred dataset citation

It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA1027447 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/)."

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