title: Detection of alternative splice and gene duplication by RNA sequencing in Japanese flounder, Paralichthys olivaceus.
abstract: 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.
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China School of Life Science, Taizhou University, Taizhou, 318000, China.
authors.forename: Wenji
authors.initials: W
authors.lastname: Wang
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Life Science, Taizhou University, Taizhou, 318000, China.
authors.forename: Feng
authors.initials: F
authors.lastname: You
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Liman
authors.initials: L
authors.lastname: Ma
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Jinning
authors.initials: J
authors.lastname: Gao
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: He
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qi
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Yu
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Wang
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China.
authors.forename: Xubo
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
authors.forename: Zhihao
authors.initials: Z
authors.lastname: Wu
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Qingdao, 266003, China qzhang@ouc.edu.cn.
authors.forename: Quanqi
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D004251:DNA Transposable Elements; D005432:Flounder / Q000235:genetics*; D020440:Gene Duplication; D016678:Genome; D006238:Haploidy; D007564:Japan; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements
keywords: Paralichthys olivaceus; alternative splicing; double haploids; gene duplication; transcriptome