Solanum nigrum genome and annotations. Plant ID=KEW Gardens 170516. 
Genome= ONT 
The genome was assembled using a combination of FLYE (version 2.1.1) to assemble the reads, RACON version 1.4.20 and MEDAKA version 1.0.3, PURGE HAPLOTIGS to phage the genome (File=S.nigrum.genome.fa)
Gene models were obtained using REPEATMODELER (version 2.1) and REPEATMASKER (version 2.1) (File=S.nigrum.genome.fa.masked) and then BRAKER (version 1.9) using proteins (Viridiplantae) and one mRNA-Seq sampled (pooled mRNA from roots, stems, leaves, flowers and berries)
Annotations were filtered by structure and function using GFACS (Version 1.1.2) and ENTAP (Files=S.nigrum.annotations.gff3, S.nigrum.annotations.gtf, S.nigrum.annotations.pep, S.nigrum.annotations.cds). 
EGGNOGG was used for the functional characterization of the gene models. (File=S.nigrum.emapper.annotations)
Methylation was called with f5c (verson 1.2) (File=all_methylation_data_genome_S.nigrum_frequency.tsv, all_methylation_data_genome_S.nigrum_nodups.tsv)
Transposable elements were annotated with Extensive de-novo TE Annotator (EDTA) (File=S.nigrum.TEanno.gff3)
NLR_nigrum_genome.txt is the NLR-Annotator output and NLR_nigrum_genome_genes is the result of bedtools intersect between the gene annotation and the NLR-Annotator output