Transposable element annotation of Septoria linicola SE15195 and SE14017

Transposable elements (TEs) were annotated on genome assemblies of Septoria linicola SE15195 (accession numbers CP099418 to CP099434) and SE14017 (accession number JAMGVY000000000), 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 22 and 21 subfamily elements according to the Wicker classification, covering 19 and 18% of the genome of SE15195 and SE14017, respectively. More informations on Septoria linicola genomes SE15195 and SE14017 can be retrieved at https://bioinfo.bioger.inrae.fr/ (BioinfoBioger website) Direct link for SE15195 genome on BioinfoBioger website: SE15195 Direct link for SE14017 genome on BioinfoBioger website: SE14017