Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690bp and N50 of 1263bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
Highlights
The Chinese giant salamander (A. davidianus) is the largest extant amphibian in the world [1,2]
Our results provide a global view of the transcriptome and pave the way for further functional characterization of A. davidianus
N50 of Transcripts or unigenes was calculated by ordering all sequences, adding the lengths from longest to shortest until the summed length exceeded 50% of the total length of all sequence
Summary
The Chinese giant salamander (A. davidianus) is the largest extant amphibian in the world [1,2] It is classified as an endangered species by the International Union for Conservation of Nature and Nature Resources, and is the class II state major protection species in China. In the evolution history of vertebrate, A. davidianus occupies a seat at the phylogenetic and species evolution process which is representing a transitional form that links the aquatic animals to terrestrial organisms because it has existed for > 350 million years [3]. This species has an important value in scientific research. In the past few decades, A. davidianus population has declined sharply due to deterioration of habitat, environmental pollution, climate change, infectious diseases, commercial trade and infrastructure development for human settlement [4,5]
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