Identification and characterizationof micro-RNA in Macrobrachium rosenbergii / Tan Tian Tian
MicroRNAs are ~20-22nt non protein-coding RNA regulatory genes that posttranscriptionally regulate many protein–coding genes to influence critical biological and metabolic processes. While the number of known microRNA is increasing, there is no published data for microRNA in freshwater prawns (Ma...
| Summary: | MicroRNAs are ~20-22nt non protein-coding RNA regulatory genes that posttranscriptionally
regulate many protein–coding genes to influence critical biological and
metabolic processes. While the number of known microRNA is increasing, there is no
published data for microRNA in freshwater prawns (Macrobrachium rosenbergii) a
commercially cultured and economically important food species. Through deep parallel
sequencing and an in silico data analysis approach, 327 miRNA families have been
identified from small RNA libraries with reference to both the de novo transcriptome of
M.rosenbergii obtained from RNA-Seq and to miRBase (Release 18.0, November 2011).
Based on the identified mature miRNA and recovered precursor sequences that form
appropriate hairpin structures, three conserved miRNA (miR125, miR750, miR993) and
27 novel miRNA candidates encoding messenger-like non-coding RNA have been
identified. miR-125, miR-750, G-m0002/H-m0009, G-m0005, G-m0008/H-m0016, Gm0011/
H-m0027 and G-m0015 were selected for experimental validation with stemloop
quantitative RT-PCR and were found coherent with the expression profile of deep
sequencing data as evaluated with Pearson’s correlation coefficient (r = 0.835178 for
miRNA in gill, r = 0.724131 for miRNA in hepatopancreas). Using a combinatorial
approach of pathway enrichment analysis and inverse expression relationship of miRNA
and mRNA, four co-expressed novel miRNA candidates (G-m0005, G-m0008/H-m0016,
G-m0011/H-m0027, and G-m0015) were found to be associated with energy
metabolism. In addition, the expression of the three novel miRNA candidates (G-m0005,
G-m0008/H-m0016, and G-m0011/H-m0027) were also found to be significantly
reduced at the 9 and 24 hours post infection in a controlled experiment of M.rosenbergii
challenged with infectious hypodermal and haematopoietic necrosis virus. These
findings provide a reference point to further improving the understanding of the
repertoire of crustacean miRNAs. |
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