The Catfish MicroRNAome: Identification, Annotation and Expression Profiling in Response to Bacterial Infections and Hypoxia Stress

MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important regulatory roles in multicellular organisms. miRNAs interact with mRNAs by complementing with their 3’-UTRs to suppress translation or initiate mRNA degradation.  While a large number of RNA-Seq have been conducted in catfish from various tissues, developmental stages and physiological conditions, expression data of noncoding RNA genes is limited. Generation of large-scale datasets for both coding and noncoding RNAs allow for integrated analysis of mRNA-ncRNA interaction networks. In this project, we conducted companion sequencing of small RNAs in catfish after ESC and columnaris disease infection and hypoxia stress. Over 330 million 50-bp reads were generated, ~25 million reads for each sample.  A total of 706 miRNA genes were identified from the channel catfish genome using homology-based and sequencing-based approaches with the programs of MapMi and miRDeep2.   Bioinformatic analysis identified 29, 17, and 15 differentially expressed miRNA genes after ESC infection, after columnaris infection and after hypoxia treatment, respectively, with distinct expression patterns. Correlated gene expression analysis of differentially expressed miRNAs revealed sets of negatively correlated expression of miRNAs and protein-coding genes, suggesting the potential target genes for the miRNAs.  Potential mechanisms for the induced and correlated expression were investigated, providing insights into miRNA-mRNA interaction networks in response to bacterial infections and hypoxic stress. This work should be valuable to develop catfish genome expression Atlas for both coding and noncoding genes, and is important for the identification of biomarkers of bacterial diseases and hypoxia.