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The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora)

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Abstract

Yellow drum (Nibea albiflora) is a commercially important marine fish, which is widely distributed in the coastal waters of China, Japan and Korea. Wild yellow drum resources have dramatically declined due to overfishing and ocean pollution. Genetic data can contribute to biodiversity conservation and protection. And molecular markers can play important roles in genetic breeding and aid in germplasm preservation in fish. In this study, 11 tissues (brain, heart, liver, kidney, muscle, head kidney, skin, fin, spleen, gonad and air bladder) were collected for pooled RNA sequencing. The unigenes were assembled using Trinity and EvidentialGene, and were then aligned to nr, nt, Swiss-Prot GO, KEGG, and KOG for annotation. Molecular markers (e.g. simple sequence repeat, SSR and single nucleotide polymorphism, SNP) were detected using MIcroSAtellite identification tool (MISA) and Genome Analysis Tool Kit (GATK). All clean reads were assembled into 109,209 transcripts, and 31,183 unigenes were generated after pruning and classifying, ranging from 201 to 19,857 bp in length (1230 bp in average), and 26,728 (85.7%) assembled unigenes had significant hits in public databases. Total of 27 and 103 unigenes were respectively identified as involved in growth- and immune-related pathways in the N. albiflora transcriptome. In addition, we identified a considerable quantity of molecular markers, including 11,484 SSRs and 56,186 SNPs. The growth- and immune-relevant genes and the molecular markers identified here provided a meaningful reference gene set and laid a foundation for future genetic selection and breeding for this species.

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Acknowledgements

This research was supported by grants from the Key Projects of the Xiamen Southern Ocean Research Centre (14GZY70NF34), the Key Projects of the Fujian Science and Technology (2014N5011) and the Projects of the Fujian Science and Technology (2014R0110).

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Authors and Affiliations

  1. Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China

    Zhaofang Han, Shijun Xiao, Wanbo Li, Kun Ye & Zhi Yong Wang

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China

    Zhi Yong Wang

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  1. Zhaofang Han
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  2. Shijun Xiao
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  3. Wanbo Li
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  4. Kun Ye
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Correspondence to Zhi Yong Wang.

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Conflict of interest

Z.H. declares that he does not have conflict of interest. S.X. declares that he does not have conflict of interest. W.L. declares that he does not have conflict of interest. K.Y. declares that he does not have conflict of interest. Z.W. declares that he does not have conflict of interest.

Ethics approval

The study was approved by the Animal Care and Use Committee of Fisheries College of Jimei University, and all experimental procedures were conducted in conformity with institutional guidelines for the care and use of laboratory animals.

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Han, Z., Xiao, S., Li, W. et al. The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora). Genes Genom 40, 881–891 (2018). https://doi.org/10.1007/s13258-018-0697-x

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  • DOI: https://doi.org/10.1007/s13258-018-0697-x

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