Identification of known and novel miRNAs
Our sncRNA sequencing returned 634.7 million reads across 73 libraries (8.7M ± 2.1M reads library-1). Of those reads, 505.1 million passed qc (6.9M ± 2.2M reads library-1), and 19.7 million, or 3.1%, were identified as miRNAs (0.27M ± 0.16M reads library-1). Similar small fractions of identified miRNAs are commonly obtained from sncRNA datasets (Jain, Rana, Tridibes, Sunil, & Bhatnagar, 2015). Based on the length distribution of each sample, there is a peak in all abdomen samples ~ 33 nt in length, which were absent in the head tissue samples (Table S1). This peak likely corresponds to tRNA fragment length (Kang et al., 2018), and highlights that there may be an abundance of tRNAs present in these tissues or they may be serving an alternative function (Su, Wilson, Kumar, & Dutta, 2020). Using miRTrace, we identified that all miRNAs detected were 100% insect specific miRNAs, indicating that there is likely no detectable contamination in any of the samples used (Table S1).
In total, we identified 188 candidate miRNAs in P. napi , of which 129 were novel and 59 were identified based on known mature read sequences in B. mori or H. melpomene . Including both 3’ and 5’ sequences of each miRNAs totaled to 257 expressed miRNAs in our samples (Table S2). Of these 257 miRNAs, 236 were identified in the head and 207 in the abdomen, with 205 shared between the tissues (Table S3).