Abstract
Northern snakehead, Ophiocephalus argus Cantor, is an endemic freshwater fish in China. However, wild stocks of O. argus are dwindling sharply. Further, water conservancy projects, environmental pollution and human activities have caused the decrease of wild stocks, which has attracted much attention. Here, we have investigated the genomic information of O. argus using IlluminaHiseq 4000 sequencing. The transcriptomes of O. argus were sequenced by Illumina technology. A total of 67,564 sequences from 79,500,964 paired-end reads were generated, 33,710 unigenes were annotated based on protein databases (NCBI nonredundant (NR) databases). In total, 7182 unigenes had the clusters of orthologous group (COG) classifications, 33,710 unigenes were assigned to 59 gene ontology (GO) terms. Further, a total of 21,464 simple sequence repeats (SSRs) from 67,564 unigenes and 113,518 single-nucleotide polymorphism (SNP) sites among 335 Mclean reads were yielded for O. argus based on a transcriptome-wide search. The new transcriptome data which is presented in this study for O. argus will provide valuable information for gene discovery and downstream applications, such as phylogenetic analysis, gene-expression profiling and identification of genetic markers (SSRs and SNP).
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References
Buermans H. P. and den Dunnen J. T. 2014 Next generation sequencing technology: advances and applications. BBA Biomembr. 1842, 1932–1941.
Chepelev I., Wei G., Tang Q. and Zhao K. 2009 Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res. 37, e106.
Christmas M. J., Biffin Ed and Lowe A. J. 2015 Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaeaviscosa. BMC Genom. 6, 803.
Cirulli E. T., Singh A., Shianna K. V., Ge D., Smith J. P., Maia J. M. et al. 2010 Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol. 11, R57.
Corredor-Ada’mez M., Welten M. C. M., Spaink H. P., Jeffery J. E., Schoon R. T., de Bakker M. A. G. et al. 2005 Genomic annotation and transcriptome analysis of the zebrafish (Daniorerio) hox complex with description of a novel member, hoxb13a. Evol. Dev. 7, 362–375.
Grabherr M. G., Hass B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I. et al. 2011 Full-length transcriptions assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652.
Houston R., Taggart J., Cézard T., Bekaert M., Lowe N., Downing A. et al. 2014 Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmosalar). BMC Genom. 15, 90.
Howe K., Clark M. D., Torroja C. F., Torrance J., Berthelot C., Muffato M. et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503.
Huang Z. P. 2011 The culture technique of Channaargus in pond. J. Aquac. 2, 37–38 (in Chinese).
Johansen S. D., Karlsen B. O., Furmanek T., Andreassen M., Jørgensen T. E., Bizuayehu T. T. et al. 2011 RNA deep sequencing of the Atlantic cod transcriptome. Comp. Biochem. Phys. D. 6, 18–22.
Landis G. A. M., Lapointe N. W. R. and Angermeier P. L. 2011 Individual growth and reproductive behavior in a newly established population of northern snakehead (Channaargus), Potomac river, USA. Hydrobiologia 661, 123–131.
Le Cam A., Bobe J., Bouchez O., Cabau C., Kah O., Klopp C. et al. 2012 Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach. Genes 500, 32–39.
Li D. Y., Kang D. H., Yin Q. Q., Sun X. W. and Liang L. Q. 2007 Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinuscarpio L.) populations. J. Genes Genom. 34, 984–993.
Li H. J., Zhang J. J., Li H. B., Gao X. G. and He C. B. 2014 Development and characterization of 13 polymorphic microsatellite markers for the Chinese surf clam (Mactrachinensis) through Illumina pairedend sequencing. Conserv. Genet. Res. 6, 877–879.
Li H. J., Liu M., Ye S. and Yang F. 2017a De novo assembly, gene annotation, and molecular marker development using Illumina paired-end transcriptome sequencing in the clam Saxidomuspurpuratus. Genes Genom. 39, 675–685.
Li X., Ou Y. S., Wu X. P., Dai Y. G., Hua Y. Q. and Jiao L. 2010 Studies on the EST and LDH isozymes in different tissues of Ophiocephalusargus in Poyang lake. Hubei Agric. Sci. 49, 153–155 (in Chinese).
Li Y. H., Wang H. P., Yao H., O’Bryant P., Rapp D., Guo L. et al. 2017b De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Percaflavescens. PLos ONE 12, e0171187.
Nie G. X., Fu Y. R., Zhang H. and Wei X. J. 2002 The analysis of nutrition components in the muscle of Channaargus. Freshw. Fish 32, 46–47 (in Chinese).
Pereiro P., Balseiro P., Romero A., Dios S., Forn-Cuni G., Fuste B. et al. 2012 High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. PLoS One 7, e35369.
Sadamoto H., Takahashi H., Okada T., Kenmoku H., Toyota M. and Asakawa Y. 2012 De novo sequencing and transcriptome analysis of the central nervous system of mollusc Lymnaeastagnalis by deep RNA sequencing. PLoS One 7, e42546.
Singh R., Kumar R., Mahato A. K., Paliwal R., Singh A. K., Kumar S. et al. 2016 De novo transcriptome sequencing facilitates genomic resource generation in Tinosporacordifolia. Funct. Integr. Genom. 16, 581–591.
Wan Q. Y. and Su J. G. 2015 Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella). Sci. Rep. 5, 12946.
Wang Y., Lu Y., Zhang Y., Ning Z. M., Li Y., Zhao Q. et al. 2015 The draft genome of the grass carp (Ctenopharyngodonidellus) provides insights into its evolution and vegetarian adaptation. Nat. Genet. 47, 625–631.
Wu L. F., Zhang D. M., Huang Q. and Liu C. L. 2000 The food analysis, population resources and utilization of snakehead fish (Ophiocephalusargus) in Huanghualake. J. Jilin Agric. Univ. 22, 104–106 (in Chinese).
Xiao M. S., Cui F., Kang J. and Zhang X. H. 2013 Genetic structure and variation of wild Ophiocephalusargus Cantor from Huaiheriver based on mtDNA D-loop sequences. J. Huazhong Normal Univ. (Nat. Sci.) 47, 82–90 (in Chinese).
Xiao M. S., Hu Q. S., Zhao Y., Bao F. Y., Cui F. and Zheng R. Q. 2018 Development of 36 SNP markers in Ophiocephalusargus Cantor based on highthroughput sequencing. Conserv. Genet. Res. 10, 35–38.
Xiao M. X., Xia H. and Bao F. 2015 Isolation and characterization of 15 microsatellite loci for Ophiocephalusargus Cantor. Russ. J. Genet. 51, 1044–1047.
Xu P., Zhang X. F., Wang X. M., Li J. T., Liu G. M., Kuang Y. Y. et al. 2014 Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat. Genet. 46, 1212–1219.
Acknowledgements
This study was supported by the Natural Science Foundation of Anhui Province, China (no. 1708085MC78), Anhui Province Key Research and Development Plan Project, China (no.1804a07020119).
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Xiao, M., Bao, F., Zhao, Y. et al. Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus. J Genet 98, 49 (2019). https://doi.org/10.1007/s12041-019-1086-1
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DOI: https://doi.org/10.1007/s12041-019-1086-1