title: RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing.
abstract: The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp). Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR). The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China; Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an, Shaanxi, 710086, China.
authors: Fenggang
authors: F
authors: Li
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Lixin
authors: L
authors: Wang
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Qingjing
authors: Q
authors: Lan
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Hui
authors: H
authors: Yang
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Yang
authors: Y
authors: Li
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Xiaolin
authors: X
authors: Liu
authors: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, 712100, China.
authors: Zhaoxia
authors: Z
authors: Yang
mesh_terms: D000818:Animals; D002681:China; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D007107:Immune System; D037102:Lectins / Q000235:genetics; D053308:Lymphotoxin-beta / Q000235:genetics; D058977:Molecular Sequence Annotation; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome; D014562:Caudata / Q000235:genetics* / Q000276:immunology; D023083:beta-Defensins / Q000235:genetics
chemical_list: D037102:Lectins; D053308:Lymphotoxin-beta; D023083:beta-Defensins; C027112:fucose-binding lectin