BRAKER Annotations for Phytophthora Genomes and Transcriptomes

File Contents: Phytophthora_BRAKER_Annotations.zip: Contains BRAKER3 output annotation files across 38 genomes and 3 transcriptomes from 2 datasets (see detailed breakdown below). Codes_for_Processing_Data.zip: Accompanying data processing scripts used to execute assemblies, filter annotations, predict effectors, and carry out functional profiling (CAZymes, peptidases, transporters, and metabolic pathways). Gene models were predicted using the BRAKER3 (v3.0.8) pipeline (Gabriel et al., 2024) within a Singularity container. For species lacking RNA-seq data, the pipeline defaulted to the ProtHint workflow. Three distinct evidence models were generated: Model 1: Utilized protein evidence from five Phytophthora reference genomes: Phytophthora infestans (GCF_000142945.1) Phytophthora nicotianae (GCF_000247585.1) Phytophthora sojae (GCF_000149755.1) Phytophthora ramorum (GCF_020800215.1) Phytophthora cinnamomi (GCF_018691715.1) Model 2: Expanded protein evidence to include both Phytophthora and downy mildew (Peronospora) references: Peronospora effusa (GCA_021491655.1) Peronospora belbahrii (GCA_920618645.1) Peronospora matthiolae (ERX11799663) Peronospora farinosa (GCA_947646735.1) Model 3: Integrated the expanded protein evidence (Model 2) with species-specific RNA-seq data for three species: Phytophthora cactorum (SRR17982083) Phytophthora nicotianae (SRR32562122) Phytophthora palmivora (SRR12759716) Note: Models 1 and 2 were also run on these three species as an internal validation check. Transcripts were selected based on BRAKER3's criteria for sufficient annotation evidence.