These are the different genome references (fasta formats) available for: Solanum lycopersicum (assemblies 3.0 and 4.0): S_lycopersicum_chromosomes.3.00.fa.tar.gz S_lycopersicum_chromosomes.4.00.fa.tar.gz Solanum pennellii (one version only from Bolger et al., 2014) : Spenn.fasta.tar.gz Solanum habrochaites LA1777 (technology hotel project 2018): LA1777.final.fasta Solanum habrochaites PI127826 (technology hotel project 2018): PI127826.final.fasta Solanum habrochaites LYC4 (from the paper of Aflitos et al. 2014. 3rd assembly version). S_habrochaites_LYC4... The two genome assemblies of S. habrochaites LA1777 and PI127826 were obtained through a combination of 10X Linked-Reads and BioNano Optical Mapping. This sequencing has been funded by the DTL Technology Hotel 2018 funding scheme. Reference: Tomato Genome Sequencing Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature volume 485, pages 635–641. Bolger et al. 2014. The genome of the stress-tolerant wild tomato species Solanum pennellii http://www.nature.com/ng/journal/v46/n9/full/ng.3046.html Hosmani et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. https://www.biorxiv.org/content/10.1101/767764v1 Aflitos et al. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616