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...
Main Authors: | , , , , , , |
---|---|
Format: | Dataset |
Language: | English |
Published: |
Dryad
2018
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.9gd3n |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::9a6645d36ce5b818ab83fb011e306346 |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::9a6645d36ce5b818ab83fb011e306346 2023-05-15T15:31:13+02:00 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 en eng Dryad http://dx.doi.org/10.5061/dryad.9gd3n https://dx.doi.org/10.5061/dryad.9gd3n lic_creative-commons 10.5061/dryad.9gd3n oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:98326 oai:easy.dans.knaw.nl:easy-dataset:98326 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c comparative transcript analysis RNA-seq Hucho taimen positive selection microsatellite markers Life sciences medicine and health care (:tba) envir scipo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2018 fttriple https://doi.org/10.5061/dryad.9gd3n 2023-01-22T16:51:54Z 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 annotationThe taimen transcirptome was annotated using Trinotate(https://trinotate.github.io/) according to the guidance. NR, Uniprot-Sprot and Pfam databases were used.Trinotate.tsv.zipInterproscan annotationInterproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan.Interproscan.tsv.zipGene Ontology ... Dataset Atlantic salmon Hucho taimen Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
comparative transcript analysis RNA-seq Hucho taimen positive selection microsatellite markers Life sciences medicine and health care (:tba) envir scipo |
spellingShingle |
comparative transcript analysis RNA-seq Hucho taimen positive selection microsatellite markers Life sciences medicine and health care (:tba) envir scipo 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 RNA-seq Hucho taimen positive selection microsatellite markers Life sciences medicine and health care (:tba) envir scipo |
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 annotationThe taimen transcirptome was annotated using Trinotate(https://trinotate.github.io/) according to the guidance. NR, Uniprot-Sprot and Pfam databases were used.Trinotate.tsv.zipInterproscan annotationInterproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan.Interproscan.tsv.zipGene Ontology ... |
format |
Dataset |
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 |
Dryad |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.9gd3n |
genre |
Atlantic salmon Hucho taimen |
genre_facet |
Atlantic salmon Hucho taimen |
op_source |
10.5061/dryad.9gd3n oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:98326 oai:easy.dans.knaw.nl:easy-dataset:98326 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.9gd3n https://dx.doi.org/10.5061/dryad.9gd3n |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.9gd3n |
_version_ |
1766361711542009856 |