Annotation of the genome assembly Noccaea caerulescens cira v2.3

The N. caerulescens cira genome assembly v2.3 was annotated using the OmicsBox suite v. 1.4.12 (www.biobam.com/omicsbox). Repetitive elements were masked using the Repeat Masking tool based on RepeatMasker v. 4.0.9 with the custom repetitive elements sequence library generated with RepeatModeler v. 2.0.1. Genes were then annotated using the Eukaryotic Gene Finder tool, based on AUGUSTUS v. 3.4.0 in which we used Arabidopsis thaliana as a model to predict coding sequences and UTR and use N. caerulescens Firmiensis RNA-Seq samples as RNA-Seq hints. The coding sequences of annotated genes were blasted (Blastp; E-value ≤ 10-5) to the ref seq_protein database limited to the Brassicaceae family and classified into protein families using InterProScan. Putative functions were annotated by Gene Ontology using Blast2GO. In addition, the function of predicted proteins was annotated with Mercator4 v2.0