De novo Assembly of the Grass Carp Ctenopharyngodon idella Transcriptome to Identify miRNA Targets Associated with Motile Aeromonad Septicemia

• DOI: 10.1371/journal.pone.0112722
• Publication Date: 2014-11-20T04:37:44Z
• Authors: Xiaoyan Xu; Yubang Shen; Jianjun Fu; Liqun Lu; Jiale Li
• Keywords: Grass carp; Sequence assembly

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 these differentially poses major challenge this non-model organism. Results Two cDNA libraries constructed mRNAs C. idella were sequenced Illumina Hiseq 2000 technology. A total more than 100 million reads generated de assembled into 199,593 transcripts which further extensively annotated comparing their sequences to different protein databases. Biochemical pathways predicted transcript sequences. BLASTx analysis against non-redundant database revealed that 61,373 unigenes coded 28,311 proteins. showed 721 at significantly levels; 475 up-regulated 246 down-regulated the SG compared RG samples. The computational prediction targets genes 188 as 5 conserved 4 putative novel families. Conclusion This study demonstrates feasibility identifying analysis. assembly data represent substantial increase genomic resources available will provide insights gene expression profile function annotations studies.