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Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus

Japanese flounder (Paralichthys olivaceus) is one of the economic important fish in China. Sexual dimorphism, especially the different growth rates and body sizes between two sexes, makes this fish a good model to investigate mechanisms responsible for such dimorphism for both fundamental questions...

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Autores principales: Wang, Wenji, Wang, Jing, You, Feng, Ma, Liman, Yang, Xiao, Gao, Jinning, He, Yan, Qi, Jie, Yu, Haiyang, Wang, Zhigang, Wang, Xubo, Wu, Zhihao, Zhang, Quanqi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267937/
https://www.ncbi.nlm.nih.gov/pubmed/25512620
http://dx.doi.org/10.1534/g3.114.012138
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author Wang, Wenji
Wang, Jing
You, Feng
Ma, Liman
Yang, Xiao
Gao, Jinning
He, Yan
Qi, Jie
Yu, Haiyang
Wang, Zhigang
Wang, Xubo
Wu, Zhihao
Zhang, Quanqi
author_facet Wang, Wenji
Wang, Jing
You, Feng
Ma, Liman
Yang, Xiao
Gao, Jinning
He, Yan
Qi, Jie
Yu, Haiyang
Wang, Zhigang
Wang, Xubo
Wu, Zhihao
Zhang, Quanqi
author_sort Wang, Wenji
collection PubMed
description Japanese flounder (Paralichthys olivaceus) is one of the economic important fish in China. Sexual dimorphism, especially the different growth rates and body sizes between two sexes, makes this fish a good model to investigate mechanisms responsible for such dimorphism for both fundamental questions in evolution and applied topics in aquaculture. However, the lack of “omics” data has hindered the process. The recent advent of RNA-sequencing technology provides a robust tool to further study characteristics of genomes of nonmodel species. Here, we performed de novo transcriptome sequencing for a double haploid Japanese flounder individual using Illumina sequencing. A single lane of paired-end sequencing produced more than 27 million reads. These reads were assembled into 107,318 nonredundant transcripts, half of which (51,563; 48.1%) were annotated by blastx to public protein database. A total of 1051 genes that had potential alternative splicings were detected by Chrysalis implemented in Trinity software. Four of 10 randomly picked genes were verified truly containing alternative splicing by cloning and Sanger sequencing. Notably, using a doubled haploid Japanese flounder individual allow us to analyze gene duplicates. In total, 3940 “single-nucleotide polymorphisms” were detected form 1859 genes, which may have happened gene duplicates. This study lays the foundation for structural and functional genomics studies in Japanese flounder.
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spelling pubmed-42679372014-12-23 Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus Wang, Wenji Wang, Jing You, Feng Ma, Liman Yang, Xiao Gao, Jinning He, Yan Qi, Jie Yu, Haiyang Wang, Zhigang Wang, Xubo Wu, Zhihao Zhang, Quanqi G3 (Bethesda) Investigations Japanese flounder (Paralichthys olivaceus) is one of the economic important fish in China. Sexual dimorphism, especially the different growth rates and body sizes between two sexes, makes this fish a good model to investigate mechanisms responsible for such dimorphism for both fundamental questions in evolution and applied topics in aquaculture. However, the lack of “omics” data has hindered the process. The recent advent of RNA-sequencing technology provides a robust tool to further study characteristics of genomes of nonmodel species. Here, we performed de novo transcriptome sequencing for a double haploid Japanese flounder individual using Illumina sequencing. A single lane of paired-end sequencing produced more than 27 million reads. These reads were assembled into 107,318 nonredundant transcripts, half of which (51,563; 48.1%) were annotated by blastx to public protein database. A total of 1051 genes that had potential alternative splicings were detected by Chrysalis implemented in Trinity software. Four of 10 randomly picked genes were verified truly containing alternative splicing by cloning and Sanger sequencing. Notably, using a doubled haploid Japanese flounder individual allow us to analyze gene duplicates. In total, 3940 “single-nucleotide polymorphisms” were detected form 1859 genes, which may have happened gene duplicates. This study lays the foundation for structural and functional genomics studies in Japanese flounder. Genetics Society of America 2014-11-05 /pmc/articles/PMC4267937/ /pubmed/25512620 http://dx.doi.org/10.1534/g3.114.012138 Text en Copyright © 2014 Wang et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Wang, Wenji
Wang, Jing
You, Feng
Ma, Liman
Yang, Xiao
Gao, Jinning
He, Yan
Qi, Jie
Yu, Haiyang
Wang, Zhigang
Wang, Xubo
Wu, Zhihao
Zhang, Quanqi
Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title_full Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title_fullStr Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title_full_unstemmed Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title_short Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
title_sort detection of alternative splice and gene duplication by rna sequencing in japanese flounder, paralichthys olivaceus
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267937/
https://www.ncbi.nlm.nih.gov/pubmed/25512620
http://dx.doi.org/10.1534/g3.114.012138
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