Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing
Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confi...
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ftdoajarticles:oai:doaj.org/article:21434481017141a2bb492821f0f803fa 2023-05-15T15:32:55+02:00 Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing Sixin Liu Guangtu Gao Ryan M. Layer Gary H. Thorgaard Gregory D. Wiens Timothy D. Leeds Kyle E. Martin Yniv Palti 2021-02-01T00:00:00Z https://doi.org/10.3389/fgene.2021.639355 https://doaj.org/article/21434481017141a2bb492821f0f803fa EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fgene.2021.639355/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2021.639355 https://doaj.org/article/21434481017141a2bb492821f0f803fa Frontiers in Genetics, Vol 12 (2021) rainbow trout structural variants copy number variants transposable elements repetitive sequence whole-genome sequencing Genetics QH426-470 article 2021 ftdoajarticles https://doi.org/10.3389/fgene.2021.639355 2022-12-31T05:16:58Z Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles Pacific Frontiers in Genetics 12 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
rainbow trout structural variants copy number variants transposable elements repetitive sequence whole-genome sequencing Genetics QH426-470 |
spellingShingle |
rainbow trout structural variants copy number variants transposable elements repetitive sequence whole-genome sequencing Genetics QH426-470 Sixin Liu Guangtu Gao Ryan M. Layer Gary H. Thorgaard Gregory D. Wiens Timothy D. Leeds Kyle E. Martin Yniv Palti Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
topic_facet |
rainbow trout structural variants copy number variants transposable elements repetitive sequence whole-genome sequencing Genetics QH426-470 |
description |
Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies. |
format |
Article in Journal/Newspaper |
author |
Sixin Liu Guangtu Gao Ryan M. Layer Gary H. Thorgaard Gregory D. Wiens Timothy D. Leeds Kyle E. Martin Yniv Palti |
author_facet |
Sixin Liu Guangtu Gao Ryan M. Layer Gary H. Thorgaard Gregory D. Wiens Timothy D. Leeds Kyle E. Martin Yniv Palti |
author_sort |
Sixin Liu |
title |
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
title_short |
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
title_full |
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
title_fullStr |
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
title_full_unstemmed |
Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing |
title_sort |
identification of high-confidence structural variants in domesticated rainbow trout using whole-genome sequencing |
publisher |
Frontiers Media S.A. |
publishDate |
2021 |
url |
https://doi.org/10.3389/fgene.2021.639355 https://doaj.org/article/21434481017141a2bb492821f0f803fa |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Frontiers in Genetics, Vol 12 (2021) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fgene.2021.639355/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2021.639355 https://doaj.org/article/21434481017141a2bb492821f0f803fa |
op_doi |
https://doi.org/10.3389/fgene.2021.639355 |
container_title |
Frontiers in Genetics |
container_volume |
12 |
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1766363406618591232 |