Genomics/technical resourcesIn-depth transcriptome analysis of Coilia ectenes, an important fish resource in the Yangtze River: de novo assembly, gene annotation
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.
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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).
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Full-length transcriptome of anadromous Coilia nasus using single molecule real-time (SMRT) sequencing
2022, Aquaculture and FisheriesCitation Excerpt :Ovaries and testes are going to develop as C. nasus migrates into fresh water (Li et al., 2007; Xu et al., 2016; Zhou et al., 2015). Unfortunately, due to overfishing, environmental pollution and other anthropogenic activities, the natural resources of C. nasus have plummeted (Shen et al., 2015). Fundamental researches are thus essential for this high-valued species to be well conserved or managed and sustainably exploited in the future.
Metabolic mechanisms of Coilia nasus in the natural food intake state during migration
2020, GenomicsCitation Excerpt :Coilia nasus is a commercially valuable species of high economic importance in China, ranking first among the “three delicacies of the Yangtze River”. Unfortunately, C. nasus populations in the Yangtze River have been decimated by overfishing and changes to the aquatic ecology [16–19]. The annual catch now is only about 2% of historical maximums [20].
Regulation of signal transduction in Coilia nasus during migration
2020, GenomicsCitation Excerpt :Their offspring move to the estuaries where they will remain until the autumn, and then migrate to the ocean for growth and fattening [3,4]. The research on C. nasus has mainly focused on nutrition and artificial culture, two areas in which the species plays important roles [5–9]. However, in terms of the molecular regulatory mechanisms of C. nasus during migration, only transcriptome analyses of the ovaries, testes, and olfactory epithelium, and key regulatory gene cloning have been completed [10–13].
Cyt b gene and D-loop sequence analyses of Coilia nasus from the Rokkaku River of Japan
2019, Regional Studies in Marine ScienceCitation Excerpt :Many Chinese researchers now use C. nasus as the scientific name for both populations in China and Japan (e.g., Gao et al., 2014; Han et al., 2015; Yang et al., 2011) and C. ectenes is believed to be synonymous with C. nasus. Nevertheless, C. ectenes has still been used in many recent papers, e.g., Zheng et al. (2015), Shen et al. (2015), and Yu et al. (2019), probably just to highlight that their anchovy samples were from Chinese waters. C. nasus from China is widely distributed along the Yangtze River and its affiliated lakes, as well as coastal waters and other tributaries (Jiang et al., 2012).
Transcriptome and metabolome analyses of Coilia nasus in response to Anisakidae parasite infection
2019, Fish and Shellfish ImmunologyCitation Excerpt :The estuarine tapertail anchovy (Coilia nasus), also known as the anadromous Japanese grenadier anchovy, is distributed in the Yangtze River, the coastal waters of China and Korea, and the Ariake Sound of Japan [1–6].