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. 2014 Jan 31;9(1):e87940.
doi: 10.1371/journal.pone.0087940. eCollection 2014.

Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers

Rongbo Che  1 , Yuena Sun  1 , Rixin Wang  1 , Tianjun Xu  1
Affiliations

Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers

Rongbo Che et al. PLoS One. .

Abstract

Background: The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it.

Principal findings: We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs).

Conclusion: This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Size distribution of the assembled unigenes.
Figure 2
Figure 2. Comparison of the number of unigene annotations obtained from the different databases.
The number of unigene annotations hits from the Nt, Nr, Swiss-Prot and Gene databases (E-value ≤1E-5), respectively.
Figure 3
Figure 3. Characteristics of homology search of assembled unigenes against Nr protein database.
(A) FPKM distribution for each assembled unigene. (B) Score distribution of BLAST hits for each unigene with a cutoff E-value of 1E-5. (C) E-value distribution of BLAST hits for each unigene with a cutoff E-value of 1E-5. (D) Identity distribution of the top BLAST hits for each unigene. (E) Similarity distribution of the top BLAST hits for each unigene. (F) Length of unigenes with hits compared with those without hits.
Figure 4
Figure 4. BLASTx top-hit species distribution of unigenes against String database.
Figure 5
Figure 5. The distribution for assembled unigenes functional classification by Gene Ontology.
(A) The distribution for assembled unigenes assigned to molecular functions, biological processes and cellular components. (B)The number of GO term annotations of each unigene was assigned.
Figure 6
Figure 6. Gene Ontology classifications of assembled unigenes.
Unigenes were assigned to three classifications: (A) molecular functions (B) cellular components and (C) biological processes.
Figure 7
Figure 7. Pathway assignment based on KEGG.
Figure 8
Figure 8. Distribution of unigenes involved in immunity.
Figure 9
Figure 9. Cathepsins gene phylogeny and amino acid alignment.
(A) Bootstrap values next to the nodes represent the percentage of 1000 replicate trees supporting the corresponding clade. (B) The predicted cathepsin proteins from H. chinensis were aligned together with X. tropicalis and X. laevis cathepsin proteins using MAFFT multiple alignment program.
Figure 10
Figure 10. SOXs gene phylogeny and amino acid alignment.
(A) Bootstrap values next to the nodes represent the percentage of 1000 replicate trees supporting the corresponding clade. (B) The predicted SOX proteins from H. chinensis were aligned together with Xenopus (Silurana) tropicalis, Xenopus laevis, Bufo marinus, Rana chensinensis and Andrias davidianus SOX proteins using DNAman multiple alignment program.
Figure 11
Figure 11. Frequency distribution of cSSRs based on motif sequence types.
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References

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Grants and funding

This study was supported by National Natural Science Foundation of China (31272661) and Zhejiang Provincial Natural Science Foundation (LY 13C 040001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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