A draft genome assembly for the heterozygous wild tomato Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors

Primary_assembly_genome_and_annotation.tar.gz & Alternative_assembly_genome_and_annotation.tar.gz:

Includes soft-masked genome sequences and final annotation sets for primary and alternative assembly. 

Primary_intermediate_annotations.tar.gz & Alternative_intermediate_annotations.tar.gz:

Includes intermediate annotation files from BRAKER and MAKER. These files could be useful if one wants to search for gene models of interest in case when the final annotation sets do not have them or proper gene models. We observed that some BUSCO genes were present in these intermediate annotation sets but not selected in the final annotation for various reasons like lack of evidence. 

10X_Genomics_assembly.tar.gz

Includes genome assemblies performed with 150 bp linked-reads from 10X Genomics Sequencing and the Supernova genome assembler. 

Solanum_habrochaites_curated_NLRs.tar.gz:

Includes NLRs manually curated from primary and alternative assemblies of S. habrochaites LA1353. NLRs from the primary assembly can be identified with "scaffold" in the sequence IDs. Sequence IDs also include classification of NLRs based on their multi-domain architecture (C: coiled-coils; R: RPW8 domain; T: TIR domain; N: NB-ARC domain; L: LRRs) and phylogenetic relationships (GT: TNL clade; GR: RNL clade; NG: not grouped into phylogenetic clades; GX: incomplete NLRs with too short NB-ARC domains and/or missing major motifs; Others: CNL groups). 

Wild_tomatoes_RenSeq.tar.gz:

Includes RenSeq data for wild tomatoes. The data include assembled contigs, MAKER annotations, and manually curated NLRs. We only curated NLRs that belong to G1, G8 and G14. RenSeq data produced from heterozygous diploid species cannot be well resolved during genome assembly, resulting in redundant contigs and gene models. The annotation sets are not processed to reflect this. To download HiFi reads, please see: