title: Transcriptomic analysis and biomarkers (Rag1 and Igμ) for probing the immune system development in Pacific cod, Gadus macrocephalus.
abstract: Mortality (>90%) is a big concern in larval rearing facilities of Pacific cod, Gadus macrocephalus, limiting its culture presently still in the experimental stages. Understanding the immune system development of G. macrocephalus is crucial to optimize the aquaculture of this species, to improve the use of economic resources and to avoid abuse of antibiotics. For the transcriptome analysis, using an Illumina sequencing platform, 61,775,698 raw reads were acquired. After a de novo assembly, 77,561 unigenes were obtained. We have classified functionally these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 27 genes mainly related to hematopoietic or lymphoid organ development and somatic diversification of immune receptors have been reported for the first time in Pacific cod, and 14 Ig heavy chain (μ chain) locuses were assembled using Trinity. Based on our previous achievement, we have chosen Rag1 and Igμ as immune system development biomarkers. Full length cDNA of Rag1 and Igμ as biomarkers were obtained respectively using RACE PCR. Concerning Rag1, the deduced amino acid of Rag1 and protein immunodetection revealed a Rag1 isoform of 69 kDa, significantly different from other fish orthologs, such as Oncorhynchus mykiss (121 kDa). Phylogenetic analysis reveals a unique immune system for the Gadus genre, not exclusive for Atlantic cod, among vertebrates. Meanwhile, full length cDNA of Igμ included an ORF of 1710 bp and the deduced amino acid was composed of a leader peptide, a variable domain, CH1, CH2, Hinge, CH3, CH4 and C-terminus, which was in accordance with most teleost. Absolute quantification PCR revealed that significant expression of Rag1 appeared earlier than Igμ, 61 and 95 dph compared to 95 dph, respectively. Here we report the first transcriptomic analysis of G. macrocephalus as the starting point for genetic research on immune system development towards improving the Pacific cod aquaculture.
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Ming-Guang
authors.initials: MG
authors.lastname: Mao
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Li
authors.affiliation: Centre d'Estudis en Biofísica, Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallés 08193, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Perálvarez-Marín
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Jie-Lan
authors.initials: JL
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China. Electronic address: zhqjiang@dlou.edu.cn.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Shi-Hui
authors.initials: SH
authors.lastname: Wen
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Hui-Qian
authors.initials: HQ
authors.lastname: Lü
mesh_terms: D000818:Animals; D017756:Aquaculture / Q000379:methods; D001483:Base Sequence; D015415:Biomarkers / Q000378:metabolism*; D015153:Blotting, Western; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D048388:Gadiformes / Q000235:genetics* / Q000276:immunology* / Q000378:metabolism; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000276:immunology* / Q000378:metabolism; D007107:Immune System / Q000254:growth & development*; D007143:Immunoglobulin Heavy Chains / Q000276:immunology* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D059467:Transcriptome / Q000276:immunology*
chemical_list: D015415:Biomarkers; D017931:DNA Primers; D018398:Homeodomain Proteins; D007143:Immunoglobulin Heavy Chains; C064658:RAG-1 protein
keywords: Development; Gadus macrocephalus; Igμ; Immune system; Rag1; Transcriptome