Transposable element annotation of Botrytis cinerea Sl3 and Vvl3

Transposable elements (TEs) were annotated on genome assemblies of Botrytis cinerea Sl3 (accession numbers CP080979-CP080996) and Vv3 (accession numbers CP080961-CP080978), 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 19 and 33 subfamily elements according to the Wicker classification, covering 4.5 and 7.7% of the genome of Sl3 and Vv3, respectively. More informations on Botrytis cinerea genomes Sl3 and Vv3 can be retrieved at https://bioinfo.bioger.inrae.fr/ (BioinfoBioger website) Direct link for Sl3 genome on BioinfoBioger website: Sl3 Direct link for Vv3 genome on BioinfoBioger website: Vv3