Ali Ali, Gao Guangtu, Al-Tobasei Rafet, Youngblood Ramey C, Waldbieser Geoffrey C, Scheffler Brian E, Palti Yniv, Salem Mohamed
Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, USA.
USDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, 25430, USA.
Sci Data. 2025 Feb 26;12(1):345. doi: 10.1038/s41597-025-04693-7.
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.
利用Canu流程、高覆盖度的PacBio长读长序列数据、Bionano光学图谱和Hi-C邻近连接序列数据，对虹鳟鱼的Swanson双单倍体（DH）YY雄性品系基因组进行了从头组装，得到了29个主要支架，与Swanson品系的核型（2N = 58）相匹配。该组装总长2.3Gb，N50为52.4Mb，在29条染色体序列中代表了约95%的基因组，支架之间仅有109个缺口。值得注意的是，对Swanson品系基因组组装中先前的错误进行了修正，包括在Omy05染色体上鉴定出一个双重大倒位（约57Mb），在Arlee和Swanson组装之间不存在Omy20倒位，以及在Omy26上发现了一个约6.7Mb的倒位。这种全面的组装有助于完善虹鳟鱼参考基因组，并为该物种未来的遗传研究提供了宝贵资源。
