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Analysis of novel immune–related genes and microsatellite markers in the transcriptome of Paphia undulata

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Abstract

Increasingly, exogenous stressors such as pathogen infections, variable water conditions, and pollution are resulting in high mortality of Paphia undulata, deleteriously affecting the quality of clam harvests. The foot is a burrowing organ in clams. Physical damage and constant contact with the external environment cause the foot to be highly sensitive to pathogen invasion and water condition variation. In the present study, the foot tissue transcriptome was analyzed to identify genes involved in immune and stress responses. The P. undulata transcriptome included 5 286 668 078 bp reads generated by Illumina Hiseq2000 sequencing and were assembled into 1 785 226 contigs by de novo method. The contigs were clustered into 99 339 transcripts and further grouped into 60 201 unigenes. Of them, 22 260 unigenes were successfully annotated using public databases. Twelve genes that were response to immune and stress were identified with abundant expression levels, including heat shock protein 70, cold shock protein, complement C3, cathepsin L, ubiquitin carboxyl–terminal hydrolase L5, and translationally controlled tumor protein. Furthermore, 566 unigenes were found homologous to genes involved in the immune response systems of pathogen discrimination, signal transduction, and immune effector, such as lectins, toll–like receptors, complement pathway, toll–like receptor signaling pathway, heat shock proteins, antioxidant enzymes, lysozymes, and mucins, indicating that P. undulata could have a complete set of innate immune mechanisms. In addition, 4 270 microsatellite markers (SSRs) were identified from 60 201 unigenes, of which trinucleotide repeats were most abundant and 16 SSRs were tested to be polymorphic. The present study provides a new insight into innate immunity and stress response mechanisms in P. undulata.

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  1. Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China

    Xiangwei Wu & Ziniu Yu

  2. Animal Science and Technology College, Yunnan Agricultural University, Kunming, 650201, China

    Xiangwei Wu

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

    Xiande Liu

  4. University of Chinese Academy of Sciences, Beijing, 100049, China

    Xiangwei Wu & Ziniu Yu

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  2. Xiande Liu
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Correspondence to Ziniu Yu.

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Supported by the Open Program of Key Laboratory of Cultivation and High–value Utilization of Marine Organisms in Fujian Province (No. 2015fjscq05), the Guangdong Province Program, China (Nos. 2014B020202011, 2016A020208011, A201601A04, 2016B020233005, 2016TQ03N905), the Science and Technology Planning Project of Guangdong Province, China (No. 2017B030314052), and the China Agriculture Research System (No. CARS–49)

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Wu, X., Liu, X. & Yu, Z. Analysis of novel immune–related genes and microsatellite markers in the transcriptome of Paphia undulata. J. Ocean. Limnol. 37, 1301–1316 (2019). https://doi.org/10.1007/s00343-019-8154-5

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