Transposable elements (TEs) were annotated on genome assemblies of Penicillum roqueforti LCP06136 (BioSample SAMN46423906) and LCP06133 (accession number GCA_030518555.1), using the REPET package (Amselem et al. 2015).

Briefly, the TEdenovo pipeline (Flutre et al. 2011) was used to detect repeated elements in the genome and to provide a consensus sequence for each family. Consensus sequences were then classified using the PASTEC tool (Hoede et al. 2014), based on the Wicker hierarchical TE classification system (Wicker et al. 2007). After manual correction, the resulting library of consensus sequences was used to annotate TE copies in the whole genome, using the TEannot pipeline (Quesneville et al. 2005). The TE annotation allowed to identification of 15 and 23 subfamily elements according to the Wicker classification, covering 3.1 and 4.7% of the genome of LCP06136 and LCP06133, respectively.

For comparative genomics studies, the 38 subfamily elements were pooled as "BULK" and used to annotate the genome assemblies of Penicillum roqueforti LCP06037, LCP06039, LCP06043 et LCP06059 (BioSamples SAMEA103939751, SAMEA103939752, SAMEA103939754, SAMEA103939755),as well as LCP06136 and LCP06133.

REPET, 3.0