Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX

doi:10.1371/journal.pone.0063741

	Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX
	Ning, Juan 1,2; Wang, Minxiao 1; Li, Chaolun1 ; Sun, Song1,3 ; Li, CL
	2013-05-06
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	8 期号:5 页码:e63741
文章类型	Article
摘要	Background: Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus.; Background: Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus. Results: Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies. Conclusion: Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.
学科领域	Science & Technology - Other Topics
DOI	10.1371/journal.pone.0063741
URL	查看原文
收录类别	SCI
语种	英语
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000321390200060
WOS关键词	GENE-EXPRESSION ; YELLOW SEA ; EGG-PRODUCTION ; RNA-SEQ ; DIAPAUSE ; FINMARCHICUS ; REPRODUCTION ; ANNOTATION ; DROSOPHILA ; DISCOVERY
WOS标题词	Science & Technology
引用统计	被引频次：46[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/337002/16503
专题	海洋生态与环境科学重点实验室
通讯作者	Li, CL
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China 3.Chinese Ecosyst Res Network, Jiaozhou Bay Marine Ecosyst Res Stn, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Ning, Juan,Wang, Minxiao,Li, Chaolun,et al. Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX[J]. PLOS ONE,2013,8(5):e63741.
APA	Ning, Juan,Wang, Minxiao,Li, Chaolun,Sun, Song,&Li, CL.(2013).Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX.PLOS ONE,8(5),e63741.
MLA	Ning, Juan,et al."Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX".PLOS ONE 8.5(2013):e63741.

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