Solanum dulcamara genome and annotations. Plant ID=KEW Gardens 39087. 
Hibrid genome= ONT + Illumina
The genome was assembled using a combination of CANU (version 2.1.1) to assemble the reads, PURGE HAPLOTIGS to phage the genome and PILON version 1.24 to polish using Illumina data (File=S.dulcamara.genome.fa)
Gene models were obtained using REPEATMODELER (version 2.1) and REPEATMASKER (version 2.1) (File=S.dulcamara.genome.fa.masked) and then BRAKER (version 1.9) combining mRNA-Seq Illumina data (5 individual samples obtained from roots, stems, leaves, flowers and berries) and \
long-cDNA models (ONT data of a pooled sample:roots, stems, leaves, flowers and berries)
TSEBRA with keep_ab_initio configuration was used to combine the results of both proteins (Viridiplantae) and mRNA-Seq predictions
Annotations were filtered by structure and function using GFACS (Version 1.1.2) and ENTAP (Files=S.dulcamara.annotations.gff3, S.dulcamara.annotations.gtf, S.dulcamara.annotations.pep, S.dulcamara.annotations.cds). 
EGGNOGG was used for the functional characterization of the gene models. (File=S.dulcamara.emapper.annotations)
Methylation was called with nanopolish (version 0.14.0) (File=all_methylation_data_genome_S.dulcamara_frequency.tsv, all_methylation_data_genome_S.dulcamara_no_dups_2.tsv)
Transposable elements were annotated with Extensive de-novo TE Annotator (EDTA) (File=S.dulcamara_genome.TEanno.gff3)
NLR_dulcamara_genome is the NLR-Annotator output and NLR_dulcamara_genome_genes is the result of bedtools intersect between the gene annotation and the NLR-Annotator output