title: De novo assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia.
abstract: BACKGROUND
  De novo transcriptome sequencing is a robust method of predicting miRNA target genes, especially for organisms without reference genomes. Differentially expressed miRNAs had been identified previously in kidney samples collected from susceptible and resistant grass carp (Ctenopharyngodon idella) affected by Aeromonas hydrophila. Target identification for these differentially expressed miRNAs poses a major challenge in this non-model organism.
  
  
  RESULTS
  Two cDNA libraries constructed from mRNAs of susceptible and resistant C. idella were sequenced by Illumina Hiseq 2000 technology. A total of more than 100 million reads were generated and de novo assembled into 199,593 transcripts which were further extensively annotated by comparing their sequences to different protein databases. Biochemical pathways were predicted from these transcript sequences. A BLASTx analysis against a non-redundant protein database revealed that 61,373 unigenes coded for 28,311 annotated proteins. Two cDNA libraries from susceptible and resistant samples showed that 721 unigenes were expressed at significantly different levels; 475 were significantly up-regulated and 246 were significantly down-regulated in the SG samples compared to the RG samples. The computational prediction of miRNA targets from these differentially expressed genes identified 188 unigenes as the targets of 5 conserved and 4 putative novel miRNA families.
  
  
  CONCLUSIONS
  This study demonstrates the feasibility of identifying miRNA targets by transcriptome analysis. The transcriptome assembly data represent a substantial increase in the genomic resources available for C. idella and will provide insights into the gene expression profile analysis and the miRNA function annotations in further studies.
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Xu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Yubang
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Fu
authors.affiliation: National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China.
authors.forename: Liqun
authors.initials: L
authors.lastname: Lu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China; E-Institute of Shanghai Universities, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, PR China.
authors.forename: Jiale
authors.initials: J
authors.lastname: Li
mesh_terms: D016980:Aeromonas hydrophila / Q000502:physiology; D000818:Animals; D002347:Carps / Q000235:genetics* / Q000382:microbiology*; D005393:Fish Diseases; D020869:Gene Expression Profiling; D015723:Gene Library; D063990:Gene Ontology; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D018805:Sepsis; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs