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

doi:10.1534/g3.114.012138

IOCAS-IR > 实验海洋生物学重点实验室

	Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
	Wang, Wenji 1,2; Wang, Jing 1; You, Feng 2; Ma, Liman 1; Yang, Xiao 1; Gao, Jinning 1; He, Yan 1; Qi, Jie 1; Yu, Haiyang 1; Wang, Zhigang 1; Wang, Xubo 1; Wu, Zhihao 3; Zhang, Quanqi 1; Zhang, QQ (reprint author), Ocean Univ China, 5 Yushan Rd, Qingdao 266003, Peoples R China.
	2014-12-01
发表期刊	G3-GENES GENOMES GENETICS
卷号	4 期号:12 页码:2419-2424
文章类型	Article
摘要	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.
关键词	Paralichthys Olivaceus Transcriptome Alternative Splicing Gene Duplication Double Haploids
学科领域	Genetics & Heredity
DOI	10.1534/g3.114.012138
收录类别	SCI
语种	英语
WOS记录号	WOS:000346341500012
引用统计	被引频次：30[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/24100
专题	实验海洋生物学重点实验室
通讯作者	Zhang, QQ (reprint author), Ocean Univ China, 5 Yushan Rd, Qingdao 266003, Peoples R China.
作者单位	1.Ocean Univ China, Coll Marine Life Sci, Key Lab Marine Genet & Breeding, Minist Educ, Qingdao 266003, Peoples R China 2.Taizhou Univ, Sch Life Sci, Taizhou 318000, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Wang, Wenji,Wang, Jing,You, Feng,et al. Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus[J]. G3-GENES GENOMES GENETICS,2014,4(12):2419-2424.
APA	Wang, Wenji.,Wang, Jing.,You, Feng.,Ma, Liman.,Yang, Xiao.,...&Zhang, QQ .(2014).Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus.G3-GENES GENOMES GENETICS,4(12),2419-2424.
MLA	Wang, Wenji,et al."Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus".G3-GENES GENOMES GENETICS 4.12(2014):2419-2424.

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