The transcriptome of the Siberian tiger (Panthera tigris altaica)

rna-seq

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, researchers at the Harbin Veterinary Research Institute 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.

Functional classification of the Siberian tiger lung unigenes

rna-seq

rna-seq

a Species distribution, identified with a homology search of the Illumina sequences in the Nr database. Tiger transcripts showed a significant similarity to those of Felis catus. b Histogram presentation of the Gene Ontology classification. The left y-axis indicates the percentage of a specific category of genes in that the main category. The right y-axis indicates the actual number of genes in that category. Based on homologous genes, 8547 unigenes were categorized into 61 GO terms. c Histogram presentation of the Clusters of Orthologous Groups (COG) classification. 10,258 unigenes were classified among the 25 COG categories. Of all the COG categories, the cluster ‘general function prediction’ contained the highest number of unigenes (3951, 39.67 %). d Histogram presentation of the KEGG enriched pathway classification. 23,449 lung unigenes were annotated in KEGG with an E value cutoff of 1.0E−5, and all these unigenes were assigned to one of the 258 KEGG pathways. The 20 most frequently annotated KEGG pathways are shown in the figure

Lu T, Sun Y, Ma Q, Zhu M, Liu D, Ma J, Ma Y, Chen H, Guan W. (2016) De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica). Mol Genet Genomics [Epub ahead of print]. [abstract]

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