ArticleG3 (Bethesda, Md.)2021
A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout.
Article in G3 (Bethesda, Md.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 79 citations in OpenAlex.
- Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss).Scientific data · 2026Article
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- Effects of Different SNP Calling and Sequence Mapping Choices on the Inference of Genetic Architecture Underlying Migration Tendency.Ecology and evolution · 2026Article
- A chromosome-level genome for gila trout (Oncorhynchus gilae) provides a novel resource for conservation and management.BMC genomics · 2026Article
- Heritable Genetic Effects Caused by a Single Generation of Captive Breeding.Evolutionary applications · 2026Article
- A genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi.The Journal of heredity · 2026Article
- Remarkable heterogeneity revealed in the genetic architecture of resistance to a key bacterial pathogen in two commercial rainbow trout populations.BMC genomics · 2025Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.BMC genomics · 2025Article
- High-density genome-wide association study points out major candidate genes for resistance to infectious pancreatic necrosis in rainbow trout.Genetics, selection, evolution : GSE · 2025Article
- Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics.Molecular ecology · 2025Article
- Intron turnover of slc26a1 and slc26a2 and convergence of intron insertion sites.Scientific reports · 2025Article
- Generation and characterization of novel transcriptome-derived SSR markers for genetic applications in blueberry.Scientific reports · 2025Article
- Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis).G3 (Bethesda, Md.) · 2025Article
- The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss.G3 (Bethesda, Md.) · 2025Article
- Genomic Insights Into Inbreeding and Adaptive Divergence of Trout Populations to Inform Genetic Rescue.Evolutionary applications · 2025Article
- Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line.Scientific data · 2025Article
- Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly.G3 (Bethesda, Md.) · 2025Article
- Genome-wide association analysis of resistance to bacterial cold-water disease in an important rainbow trout aquaculture breeding population.Frontiers in genetics · 2025Article
- In-depth investigation of genome to refine QTL positions for spontaneous sex-reversal in XX rainbow trout.PloS one · 2025Article
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is shown through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.
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