Intriguingly, about 0.35 ~ 0.95% and 5.27 ~ 9.79% of our uniquely mapped read were mapped to the antisense strand of annotated open reading frames (ORFs) and intergenic regions, respectively.
We found a total of 52 small RNA reads that spanned exon-exon junctions (51 mapped in the antisense orientation and 1 mapped in the sense orientation) and 1,187 small RNA reads that mapped to predicted introns (908 mapped in the antisense orientation and 279 mapped in the sense orientation) (Additional file 2: Table S3).
Furthermore, as shown in Figure 1, in all the samples over 90% and less than 10% of the total mapped nucleotides were mapped to the sense strand and intergenic regions, respectively, with only 0.35 ~ 0.95% of the total mapped nucleotides mapped to the antisense strand.
The LTR subfamily showed the highest piRNA association is the LTR1/HUERS-P2 elements: 20% of the piRNAs mapped to the antisense direction of LTRs mapped to these elements.
The reads mapped to the sense strand and the reads mapped to the antisense strand were separated.
In the mycelia library, 1522 14844 prorated) small RNAs mapped to the sense strand and 1883 18211 prorated) mapped to the antisense strand.
The majority of the 19% of piRNAs that did map to transposons in Ae. aegypti mapped to the antisense transcription strand, a pattern that was previously observed in D. melanogaster, and is consistent with having transposon transcripts sliced by PIWI proteins loaded with piRNAs that are antisense to the transposon transcript [ 31].
Around 99% of SMART and ENC reads mapped to the sense strand, whereas around 99% of TS reads mapped to the antisense strand, as expected according to the manufacturer's specifications.
Approximately 67% of the peach-specific miRNAs mapped to the sense strand of genome scaffolds while only 33% of them mapped to the antisense strand (Additional file 6: Table S5).
We recovered eight sequence reads that uniquely mapped to the antisense hairpin sequence of miR-306 (miR-306-AS) and a single read mapping to the antisense hairpin of miR-263 (miR-263-AS), which indicates that the antisense transcripts were processed into mature miRNAs in vivo.
