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

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, g...

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Bibliographic Details
Published in:PloS one 2014-01, Vol.9 (1), p.e87940-e87940
Main Authors: Che, Rongbo, Sun, Yuena, Wang, Rixin, Xu, Tianjun
Format: Article
Language:English
Subjects:
Adaptation
Adaptation, Physiological - physiology
Amphibians
Analysis
Animals
Annotations
Biological evolution
Biology
Databases, Nucleic Acid
DNA sequencing
Endangered & extinct species
Endangered species
Evolution & development
Evolutionary genetics
Gene expression
Gene Expression Profiling
Genes
Genetic markers
Genetic Markers - physiology
Genetics
Genome - physiology
Genomes
Genomics
Homology
Hynobius chinensis
Identification
Immune system
Laboratories
Male
Markers
Paleontology
Pollutants
Polymorphism, Single Nucleotide
Population
Population number
Reproduction
Reproduction (biology)
Reproduction - physiology
Reptiles & amphibians
Salamandridae
Sex
Sex determination
Simple sequence repeats
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Transcriptome - physiology
Wildlife conservation
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Summary: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. 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). 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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0087940