Repeat element and non-coding RNA annotation
Repeats and transposable element families in the PFM genome were first
detected by RepeatMasker v4.0.7 pipeline (Tarailo‐Graovac & Chen, 2009)
against the Insecta repeats within RepBase Update
(http://www.girinst.org) and Dfam database (20170127), with RMBlast
v2.10.0 as a search engine. The noncoding RNAs (ncRNA) were annotated by
aligning the genomic sequence against RFAM
v14.2 (http://rfam.xfam.org/) with
BLASTN. The tRNAs and rRNAs were
predicted by tRNAscan-SE and RNAmmer (Lagesen et al., 2007; Lowe &
Eddy, 1997).