Elsevier

Marine Genomics

Volume 23, October 2015, Pages 15-17
Marine Genomics

Genomics/technical resources
In-depth transcriptome analysis of Coilia ectenes, an important fish resource in the Yangtze River: de novo assembly, gene annotation

https://doi.org/10.1016/j.margen.2015.03.002Get rights and content

Abstract

Coilia ectenes is an important teleost species in the Yangtze River and a model organism that can be used to study the protection of fish resources. In this report, we performed de novo transcriptome sequencing of ten cDNA libraries from the brain, gill, heart, intestine, kidney, liver, muscle, stomach, ovary, and testis tissues. A total of 352 million raw reads of 100 base pairs were generated, and 130,113 transcripts, corresponding to 65,350 non-redundant transcripts, with a mean length of 1520 bp, were assembled. BLASTx-based gene annotation (E-value < 1 × 10 5) allowed the identification of 73,900 transcripts against at least one of four databases, including the NCBI non-redundant database, the GO database, the COG database, and the KEGG database. Our study provides a valuable resource for C. ectenes genomic and transcriptomic data that will facilitate future functional studies of C. ectenes.

Introduction

Coilia ectenes (Jordan and Seale, 1905), also known as Coilia nasus, and commonly known as the Japanese grenadier anchovy, is an important fishery resource in the Yangtze River. Indeed, C. ectenes is known locally as one of the “three Yangtze flavors”, along with Tenualosa reevesii (Reeve's shad) and Takifugu fasciatus (obscure pufferfish). C. ectenes is a member of the family Engraulidae, of the order Clupeiformes, that is widely distributed in the middle and lower Yangtze River and its affiliated lakes, where it is utilized in aquaculture (Cheng and Lu, 2005, Yuan et al., 1980). The C. ectenes harvest from the Yangtze River has decreased severely since the 1970s; annual production decreased from 3750 tons in 1973 to 12 tons in 2011 (Wei et al., 2012, Zhang et al., 2005). This situation is a result of multiple factors, including environmental pollution, overfishing, and other human activity. To protect C. ectenes in the Yangtze River, coordinated research across different fields is required, including population genetics, development and reproduction, physiology, and nutrition. Such research requires considerable background information with regard to the C. ectenes genome, but available data in this area is severely lacking.

In recent years, next generation sequencing technologies have been developed to explore the genomes of model and non-model organisms. Compared to traditional Sanger sequencing technology, next generation sequencing platforms are revolutionary in their ability to provide enormous amounts of sequence data with a greater breadth and depth of information (Metzker, 2010). Many fish have been studied using next generation sequencing technologies, including the common carp (Cyprinus carpio), the common sole (Solea solea), the Atlantic bonito (Sarda sarda), and the sea bass (Dicentrarchus labrax) (Ferraresso et al., 2013, Magnanou et al., 2014, Sarropoulou et al., 2014, Wang et al., 2012). These reports have advanced our understanding of fish genomes and gene functions. In this study, the transcriptomes of ten major organs in C. ectenes were sequenced using hi-seq sequencing technology. We believe that the data obtained from this study represent an import resource for C. ectenes research.

Section snippets

Ethics statement

This study was approved by the Animal Care and Use Committee of Freshwater Fisheries Research Center at the Chinese Academy of Fishery Sciences. All surgery was performed under sodium pentobarbital anesthesia, and all efforts were made to minimize suffering.

Illumina sequencing of ten C. ectenes tissue types

A total of twenty wild C. ectenes weighing approximately 100–200 grams each were collected from the Jiangyin section of the Yangtze River, Jiangsu Province, China. Ten tissue types (brain, gill, heart, intestine, kidney, liver, muscle,

Acknowledgments

This work was supported by a grant from the National Special Research Fund for Non-Profit Sector (201203065) and the National Key Technology R&D Program (2012BAD26B05).

References (10)

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