Data set for transcriptome analysis of the Chinese giant salamander (Andrias davidianus ).

Yuan Wang,Xuemei Jiang,Xiaoying Zhang

doi:10.1016/j.dib.2015.11.042

Yuan Wang, Xuemei Jiang + Show 1 more

Open Access

https://doi.org/10.1016/j.dib.2015.11.042

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Abstract

The Chinese giant salamander (Andrias davidianus) occupies a seat at the phylogenetic and species evolution process, which makes it an invaluable model for genetics; however, the genetic information and gene sequences about the Chinese giant salamander in public databases are scanty. Hence, we aimed to perform transcriptome analysis with the help of high-throughput sequencing. In this data, 61,317,940 raw reads were acquired from Chinese giant salamander mRNA using Illumina paired-end sequencing platform. After de novo assembly, a total of 72,072 unigenes were gained, in which 33,834 (46.95%) and 29,479 (40.91%) transcripts exhibited homology to sequences in the Nr database and Swiss-Prot database, (E-value <10−5), respectively. In the obtained unigenes, 18,019 (25%) transcripts were assigned with at least one Gene Ontology term, of which 1218 (6.8%) transcripts were assigned to immune system processes. In addition, a total of 17,572 assembled sequences were assigned into 241 predicted KEGG metabolic pathways. Among these, 2552 (14.5%) transcripts were assigned to the immune system relevant pathway and 5 transcripts were identified as potential antimicrobial peptides (AMPs).

Highlights

The Chinese giant salamander (Andrias davidianus) occupies a seat at the phylogenetic and species evolution process, which makes it an invaluable model for genetics; the genetic information and gene sequences about the Chinese giant salamander in public databases are scanty
61,317,940 raw reads were acquired from Chinese giant salamander mRNA using Illumina paired-end sequencing platform
18,019 (25%) transcripts were assigned with at least one Gene Ontology term, of which 1218 (6.8%) transcripts were assigned to immune system processes

Summary

Animal material and RNA Isolation

Two healthy Chinese giant salamanders of two ages (one-year-old and two year-old) were collected from a farm in HanZhong, Shaanxi Province, China. Total RNA was isolated from the spleen tissues using RNAsimple Total RNA Kit (Tiangen Technologies Inc., Beijing, China). The RNA integrity score and quantity was checked by RNA 6000 Nano Assay Kit with a Bioanalyzer 2100 (Agilent Technologies) prior to cDNA synthesis. Beads with oligo-dT were used to isolate poly-A mRNA after total RNA purification. The mRNA was disrupted into short fragments with fragmentation buffer [1]. These short fragments can serve as templates to synthesize first-strand cDNA by using random primers. The second-strand cDNA was synthesized using RNase H and DNA polymerase I [1]. The short fragments were linked to sequencing adapters and screened as templates by electrophoresis for PCR amplification [2]. The cDNA library was sequenced on an Illumina HiSeq2000 platform

Data filtering and de novo assembly

Findings

Gene Annotations and Classifications