Evidence map›Paper›PMID 27631966›Full record

ArticleMolecular genetics and genomics : MGG2016

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

Taofeng Lu, Yujiao Sun, Qin Ma, Minghao Zhu, Dan Liu, Jianzhang Ma, Yuehui Ma, Hongyan Chen, Weijun Guan

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Article in Molecular genetics and genomics : MGG, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

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5citing papers in PubMed
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3 · Its place in the literature

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5 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

Taofeng LuState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
Yujiao SunCollege of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China.
Qin MaState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
Minghao ZhuState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
Dan LiuHeilongjiang Northeast Tiger Park, Harbin, 150028, China.
Jianzhang MaCollege of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China.
Yuehui MaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Hongyan ChenState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China. chenhongyan@caas.cn.
Weijun GuanInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. weijunguan301@gmail.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Genetic MarkersAnimalsEndangered SpeciesExpressed Sequence TagsGene Expression ProfilingGene Regulatory NetworksHigh-Throughput Nucleotide SequencingLungMicrosatellite RepeatsMolecular Sequence AnnotationSequence Analysis, RNATigersGenetic MarkersEST-SSR markersPanthera tigris altaicaSiberian tigerTranscriptomic analysis

Identifiers

PMID27631966

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