Abstract
BackgroundThe 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 FindingsWe 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).ConclusionThis 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.
Highlights
The Chinese salamander (Hynobius chinensis), a species of salamander in the hynobiidae family, is praised as the ‘‘golden key’’ of studying paleontology evolutionary history and precious ‘‘living fossil’’
A total of 43,769,857 (98.65%) pair reads with an average length of 77 bases were yielded from 44,367,596 pair reads after quality control by basecalling, which could be used for subsequent splicing analysis (Table 1).Because of there were no assembled and annotated Chinese salamander genomic sequences could be used for transcript assembly; Trinity de novo assembler [21] was used to assemble all the trimmed reads with optimized Kmer length of 25
Evaluation and Annotation To validate and annotate the 148,510 unigenes generated by Trinity, the assembled unigenes were received to BLASTX and BLASTN searches (E-value # 1.0E-5) against public protein databases and nucleotide databases of the National Center for Biotechnology Information (NCBI)
Summary
The Chinese salamander (Hynobius chinensis), a species of salamander in the hynobiidae family, is praised as the ‘‘golden key’’ of studying paleontology evolutionary history and precious ‘‘living fossil’’. It has been listed in the China Red Data Book with the National treasure-panda in 1986 and further classified on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species since 2004. It was first described by Gunther in 1889 as Hynobius chinensis (H. chinensis) from specimens collected in Yichang, Huibei Province [1]. 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. 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
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