Identification and profiling of microRNAs of Euphausia superba using Illumina deep sequencing

MicroRNAs (miRNAs) are an abundant class of conserved, non-coding small RNAs that play important role in gene regulation at post translational level. There have been no reports on the miRNAs of the Antarctic krill Euphausia superba despite the specie's crucial position in Antarctic food webs. Two small RNA libraries were constructed from eyestalk and muscle, subsequently, and deep sequencing analysis was performed to investigate and profile E. superba miRNAs. A total of 19 304 586 and 23 005 104 unique sequences were obtained from the eyestalk and muscle, respectively. After compared the small RNA sequences with the Rfam database, 12 342 039 and 7 907 477 reads in eyestalk and muscle were matched to the transcriptome sequence of E. superba. A total of 236 distinct miRNAs were identified after annotation to known animal miRNAs registered in miRBase 21. In both libraries, the most abundant known miRNA were miR-750 with 92 583 reads in muscle and miR-1304-3p with 56 386 reads in eyestalk while the average value was less than 106, revealing a wide range of different expression levels. In addition, niR-277a enriched in both libraries and may be involved in modulating Krebs cycle by targeting to Vimar. Differential expression analysis showed that 56 mature miRNAs were significantly up/down regulated according to expression fold change. It appeared that the expression of several abundant miRNAs maybe tissue-specific or tissue-bias. Notably, the expression pattern of miR-750 and miR-1 family, which was suggested as the crucial candidates, involved in muscle development. Taken together, this study provides the first miRNA profile of E. superba and some of these miRNAs were expected to play important role in immune response, reproduction, energy metabolism, and muscle development and so on. Thus, the results provides a reference for functional studies of miRNAs in E. superba.