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De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica)

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Abstract

The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated ‘PTA-lung’) and a pooled tissue sample (designated ‘PTA’). Approximately 47.5 % (33,187/69,836) of the lung transcriptome was annotated in four public databases (Nr, Swiss-Prot, KEGG, and COG). The annotated genes formed a potential pool for gene identification in the tiger. An analysis of the genes differentially expressed in the PTA lung, and PTA samples revealed that the tiger may have suffered a series of diseases before death. In total, 1062 non-redundant SSRs were identified in the Siberian tiger transcriptome. Forty-three primer pairs were randomly selected for amplification reactions, and 26 of the 43 pairs were also used to evaluate the levels of genetic polymorphism. Fourteen primer pairs (32.56 %) amplified products that were polymorphic in size in P. tigris altaica. In conclusion, the transcriptome sequences will provide a valuable genomic resource for genetic research, and these new SSR markers comprise a reasonable number of loci for the genetic analysis of wild and captive populations of P. tigris altaica.

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Acknowledgments

The authors are grateful to the “Heilongjiang Northeast Tiger Park” administration for the authorization of sample collection, and to the two anonymous reviewers for valuable suggestions. We also thank the BGI for the high-throughput RNA-Seq. The sequencing work was supported by the project National Infrastructure of Animal Germplasm Resources (2013), and the data analysis was supported by the National Key Technology Support Program (2015BAI07B02-02).

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    Authors and Affiliations

    1. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

      Yuehui Ma & Weijun Guan

    2. State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China

      Taofeng Lu, Qin Ma, Minghao Zhu & Hongyan Chen

    3. College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China

      Yujiao Sun & Jianzhang Ma

    4. Heilongjiang Northeast Tiger Park, Harbin, 150028, China

      Dan Liu

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    1. Taofeng Lu
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    Correspondence to Hongyan Chen or Weijun Guan.

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    Funding

    The sequencing work was supported by the project National Infrastructure of Animal Germplasm Resources (2013), and the data analysis was supported by the National Key Technology Support Program (2015BAI07B02-02).

    Conflict of interest

    Taofeng Lu declares that he has no conflict of interest. Yujiao Sun declares that she has no conflict of interest. Minghao Zhu declares that he has no conflict of interest. Dan Liu declares that he has no conflict of interest. Jianzhang Ma declares that he has no conflict of interest. Yuehui Ma declares that he has no conflict of interest. Hongyan Chen declares that he has no conflict of interest. Weijun Guan declares that he has no conflict of interest.

    Ethical approval

    All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

    Data availability

    The clean reads data can be obtained from the NCBI Short Read Archive (SRA) under Accession Numbers SRR1014897 and SRR1015838.

    Additional information

    Communicated by S. Hohmann.

    T. Lu and Y. Sun contributed equally to this work.

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    Lu, T., Sun, Y., Ma, Q. et al. De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica). Mol Genet Genomics 291, 2145–2157 (2016). https://doi.org/10.1007/s00438-016-1246-4

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