Chromosome Level Genome Assembly and Annotation of the Swanson Rainbow Trout Homozygous Line

Overview

Journal Sci Data

Specialty Science

Date 2025 Feb 26

PMID 40011488

Authors

Ali Ali

Guangtu Gao

Rafet Al-Tobasei

Ramey C Youngblood

Geoffrey C Waldbieser

Brian E Scheffler

Yniv Palti

Mohamed Salem

Affiliations

Soon will be listed here.

Abstract

The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.4 Mb, represents approximately 95% of the genome in 29 chromosome sequences with only 109 gaps between scaffolds. Notably, corrections to previous errors in the Swanson line genome assembly were made, including the identification of a double large inversion on the Omy05 chromosome (~57 Mb), the absence of the Omy20 inversion between the Arlee and Swanson assemblies, and the discovery of a ~6.7 Mb inversion on Omy26. This comprehensive assembly contributes to refining the rainbow trout reference genome and serves as a valuable resource for future genetic studies within this species.

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