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De novo transcriptome analysis and antimicrobial peptides screening in skin of Paa boulengeri

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Abstract

Secretion of amphibian skins contain bioactive peptides that considered being an enormous medicine resource pending further exploitation and utilization. In this study, we found the skin secretion of Paa boulengeri exhibited stronger bacteriostatic activity when compared to H. guentheri, R. nigromaculata, and R. chensinensis, particularly against Bacillus subtilis. To discover antibacterial related genes in P. boulengeri, the cDNA library of P. boulengeri skin was constructed and subjected to RNA sequencing analysis. The assembly of the Illumina datasets was optimized using various assembly programs and parameters. The final optimized assembly generated 94,108 transcripts with an average length of 1292 bp and N50 of 2257 bp, representing 121.6 Mb of the P. boulengeri transcriptome. Among the 94,108 transcripts, 38,584 (40.1%) transcripts were annotated and 29,260 (31.1%) were matched with unique protein accessions in the Nr database. A total of 3165 potential cDNA-derived simple sequence repeats were identified, which distributed among 3034 transcripts. In addition, 177 antibacterial peptides and nine different Toll-like receptors were identified in P. boulengeri skin based on this transcriptome dataset. Moreover, some AMPs exhibited high expressions in P. boulengeri, such as Japonicin, which reflects mutual evolution between P. boulengeri and environment. These results provide a comprehensive sequence resource and molecular basis for researches on functional genomics and pharmacological activities of P. boulengeri.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (Grant No. 31501273), the Programs for Science and Technology Development of Chongqing Province (Grant Nos. cstc2012gg-yyjs80004; cstc2015jcyjBX0013), and the Foundation for High-level Talents of Chongqing University of Art and Science (No. R2014LX07).

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  1. Conservation & Development Center of Rare & Endangered Aquatic Resources, Chongqing University of Arts & Sciences, Chongqing, 402168, China

    Yusong Jiang, Wenqiao Fan & Jingming Xu

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  1. Yusong Jiang
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  2. Wenqiao Fan
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  3. Jingming Xu
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Correspondence to Jingming Xu.

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Yusong Jiang, Wenqiao Fan and Jingming Xu declare that they have no conflict of interest with the contents of the manuscript.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards established by the Chongqing University of Arts & Sciences’ IACUC committee.

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Yusong Jiang and Wenqiao Fan have contributed equally to the study.

Data accessibility: Raw sequence and the Transcriptome Shotgun Assembly data were submitted to the NCBI Short Read Archive (SRA) under Accession Numbers SRR2962603.

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Jiang, Y., Fan, W. & Xu, J. De novo transcriptome analysis and antimicrobial peptides screening in skin of Paa boulengeri . Genes Genom 39, 653–665 (2017). https://doi.org/10.1007/s13258-017-0532-9

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