title: De Novo Transcriptome Analysis Provides Insights into Immune Related Genes and the RIG-I-Like Receptor Signaling Pathway in the Freshwater Planarian (Dugesia japonica).
abstract: BACKGROUND
  The freshwater planarian Dugesia japonica (D. japonica) possesses extraordinary ability to regenerate lost organs or body parts. Interestingly, in the process of regeneration, there is little wound infection, suggesting that D. japonica has a formidable innate immune system. The importance of immune system prompted us to search for immune-related genes and RIG-I-like receptor signaling pathways.
  
  
  RESULTS
  Transcriptome sequencing of D. japonica was performed on an IlluminaHiSeq2000 platform. A total of 27,180 transcripts were obtained by Trinity assembler. CEGMA analysis and mapping of all trimmed reads back to the assembly result showed that our transcriptome assembly covered most of the whole transcriptome. 23,888 out of 27,180 transcripts contained ORF (open reading fragment), and were highly similar to those in Schistosoma mansoni using BLASTX analysis. 8,079 transcripts (29.7%) and 8,668 (31.9%) were annotated by Blast2GO and KEGG respectively. A DYNLRB-like gene was cloned to verify its roles in the immune response. Finally, the expression patterns of 4 genes (RIG-I, TRAF3, TRAF6, P38) in the RIG-I-like receptor signaling pathway were detected, and the results showed they are very likely to be involved in planarian immune response.
  
  
  CONCLUSIONS
  RNA-Seq analysis based on the next-generation sequencing technology was an efficient approach to discover critical genes and to understand their corresponding biological functions. Through GO and KEGG analysis, several critical and conserved signaling pathways and genes related to RIG-I-like receptor signaling pathway were identified. Four candidate genes were selected to identify their expression dynamics in the process of pathogen stimulation. These annotated transcripts of D. japonica provide a useful resource for subsequent investigation of other important pathways.
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.|Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Qiuxiang
authors.initials: Q
authors.lastname: Pang
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.|Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Gao
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.|Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Hu
authors.affiliation: Immolife-biotech Co., Ltd., Nanjing 210000, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: An
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.|Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Hongkuan
authors.initials: H
authors.lastname: Deng
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Yichao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Guangzhong
authors.initials: G
authors.lastname: Zhu
authors.affiliation: Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.|Shenzhen University Health Science Center, Shenzhen 518060, China.
authors.forename: Baohua
authors.initials: B
authors.lastname: Liu
authors.affiliation: Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo 255049, China.
authors.forename: Bosheng
authors.initials: B
authors.lastname: Zhao
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D053487:DEAD-box RNA Helicases / Q000235:genetics; D063990:Gene Ontology; D015801:Helminth Proteins / Q000235:genetics* / Q000276:immunology; D007109:Immunity / Q000235:genetics*; D017403:In Situ Hybridization; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010932:Planarians / Q000235:genetics* / Q000276:immunology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction / Q000235:genetics* / Q000276:immunology; D059467:Transcriptome
chemical_list: D015801:Helminth Proteins; D053487:DEAD-box RNA Helicases