Data from: De novo assembly and characterization of the Hucho taimen transcriptome
Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA-Seq is a useful tool for obtaining genetic information and developing genetic mark...
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ftzenodo:oai:zenodo.org:5007190 2024-09-09T19:30:25+00:00 Data from: De novo assembly and characterization of the Hucho taimen transcriptome Tong, Guang-Xiang Xu, Wei Zhang, Yong-Quan Zhang, Qing-Yu Yin, Jia-Sheng Kuang, Youyi Kuang, You-Yi 2018-11-29 https://doi.org/10.5061/dryad.9gd3n unknown Zenodo https://doi.org/10.1002/ece3.3735 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.9gd3n oai:zenodo.org:5007190 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode comparative transcript analysis Hucho taimen positive selection info:eu-repo/semantics/other 2018 ftzenodo https://doi.org/10.5061/dryad.9gd3n10.1002/ece3.3735 2024-07-25T20:51:49Z Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA-Seq is a useful tool for obtaining genetic information and developing genetic markers for non-model species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA-Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein-coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including 8 salmonids, and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: it possesses more immune-related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples, and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids and selective breeding for threatened taimen. Trinotate annotation The taimen transcirptome was annotated using Trinotate(https://trinotate.github.io/) according to the guidance. NR, Uniprot-Sprot and Pfam databases were used. Trinotate.tsv.zip Interproscan annotation Interproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan. Interproscan.tsv.zip Gene ... Other/Unknown Material Atlantic salmon Hucho taimen Zenodo |
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comparative transcript analysis Hucho taimen positive selection |
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comparative transcript analysis Hucho taimen positive selection Tong, Guang-Xiang Xu, Wei Zhang, Yong-Quan Zhang, Qing-Yu Yin, Jia-Sheng Kuang, Youyi Kuang, You-Yi Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
topic_facet |
comparative transcript analysis Hucho taimen positive selection |
description |
Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA-Seq is a useful tool for obtaining genetic information and developing genetic markers for non-model species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA-Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein-coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including 8 salmonids, and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: it possesses more immune-related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples, and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids and selective breeding for threatened taimen. Trinotate annotation The taimen transcirptome was annotated using Trinotate(https://trinotate.github.io/) according to the guidance. NR, Uniprot-Sprot and Pfam databases were used. Trinotate.tsv.zip Interproscan annotation Interproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan. Interproscan.tsv.zip Gene ... |
format |
Other/Unknown Material |
author |
Tong, Guang-Xiang Xu, Wei Zhang, Yong-Quan Zhang, Qing-Yu Yin, Jia-Sheng Kuang, Youyi Kuang, You-Yi |
author_facet |
Tong, Guang-Xiang Xu, Wei Zhang, Yong-Quan Zhang, Qing-Yu Yin, Jia-Sheng Kuang, Youyi Kuang, You-Yi |
author_sort |
Tong, Guang-Xiang |
title |
Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
title_short |
Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
title_full |
Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
title_fullStr |
Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
title_full_unstemmed |
Data from: De novo assembly and characterization of the Hucho taimen transcriptome |
title_sort |
data from: de novo assembly and characterization of the hucho taimen transcriptome |
publisher |
Zenodo |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.9gd3n |
genre |
Atlantic salmon Hucho taimen |
genre_facet |
Atlantic salmon Hucho taimen |
op_relation |
https://doi.org/10.1002/ece3.3735 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.9gd3n oai:zenodo.org:5007190 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.9gd3n10.1002/ece3.3735 |
_version_ |
1809899392987037696 |