Genome Assembly and Annotation of E. sativa

Genome assembly and annotation of Eruca sativa. High-molecular-weight DNA sequenced on Oxford Nanopore platforms was assembled de novo using Shasta v0.14.0, polished with POLCA using Omni-C reads, scaffolded with YaHS v1.2.2, and screened for contamination using NCBI FCS-GX v0.5.5. Repetitive elements were annotated and soft-masked using RepeatModeler v2.0 and RepeatMasker v4.2.3. Structural gene annotation was performed with BRAKER3 v3.0.8 in ETP mode, incorporating OrthoDB Viridiplantae protein homology data and six publicly available RNA-Seq datasets. Functional annotation was carried out with InterProScan v5.76-107.0 and EggNOG-mapper v2.18. Files include the final genome assembly (FASTA), predicted coding sequences (FASTA), protein sequences (FASTA), and a functionally annotated gene model file (GFF3).