Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development

miRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.Developmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.Atlantic halibut, Hippoglossus hippoglossus L., the largest flatfish of Atlantic Ocean, is a species of commercial interest to the aquaculture industry. Halibut's early developmental stages are prolonged and morphologically defined [1,2]. The critical developmental stages, when dramatic changes in signaling, physiology and morphology occur, include: (i) maternal to zygote transition (MZT), when maternally stocked transcripts are degraded and zygote transcripts take control over the development; (ii) organogenesis, when the germ layers are formed; (iii) hatching, when the embryo becomes a free-swimming larva; (iv) first feeding, when active movement, visualization, recognition of prey, and exogenous feeding begin; and (v) metamorphosis, the most dramatic morphological and behavioral change in a flatfish during the transition from a symmetric post-larval to an asymmetric juvenile stage, when migration of one eye towards the other one occurs across the skull [1].MiRNAs are small (18 - 26 nucleotides) non-coding RNAs