DOI: 10.5281/zenodo.3501122
title: Genomic sequences and annotations for Solanum lycopersicum, Solanum pennellii and Solanum habrochaites

description: <strong>=== Genome sequences === </strong> These are the different genome references (fasta formats) available for: <em>Solanum lycopersicum</em>: S_lycopersicum_chromosomes.2.50.fa.gz S_lycopersicum_chromosomes.3.00.fa.tar.gz S_lycopersicum_chromosomes.4.00.fa.tar.gz <em>Solanum pennellii </em>(one version only from Bolger et al., 2014) : Spenn.fasta.tar.gz <em>Solanum habrochaites</em> LA1777 (technology hotel project 2018): LA1777.final.fasta <em>Solanum habrochaites</em> PI127826: 2018 Hotel Project: PI127826.final.fasta 2021 Dovetails assembly: PI127826_hirise_assembly.fasta.gz <em>Solanum</em> <em>habrochaites</em> LYC4 (from the paper of Aflitos et al. 2014. 3rd assembly version): S_habrochaites_LYC4... <em>Solanum arcanum</em> LA2172 (from the paper of Aflitos et al. 2014. 3rd assembly version): LA2172.fasta.tar.gz <em>Solanum chilense</em> LA3111 (from the paper of Stam et al. 2019, NCBI assembly ASM601370v1): LA3111.fasta.tar.gz <em>Solanum lycopersicoides</em> LA2951 (from the work of The Boyce Thompson Institute and RWTH Aachen University: link): S_lycopersicoides_LA2951_v1.0_chromosomes.fasta.tar.gz 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. <strong>=== Transcriptomes and proteomes ===</strong> <em><strong>Solanum lycopersicum</strong> (assembly</em> 4.0): Transcriptome: ITAG4.0_cDNA.fasta Proteome: ITAG4.0_proteins.fasta <em><strong>Solanum pennellii</strong> </em>(one version only from Bolger et al., 2014): Transcriptome: Spenn-v2-cds-annot.fa Proteome: Spenn-v2-aa-annot.fa <strong><em>Solanum lycopersicoides</em></strong> (version 1.0) Transcriptome: S_lycopersicoides_LA2951_v1.0_cds.fasta Proteome: S_lycopersicoides_LA2951_v1.0_proteins.fasta <strong><em>Solanum habrochaites </em>PI127826 </strong> <strong>Transcriptome: </strong>Solanum_habrochaites_PI12826_mRNAs.fasta (2018 Hotel Project assembly) <strong>Transcriptome (2021 Dovetails): </strong>Solanum_habrochaites_PI127826_CDS_Dovetails_2021.fasta <strong>Proteome (2021 Dovetails): </strong>Solanum_habrochaites_PI127826_protein_Dovetails_2021.fasta<strong> </strong> <strong>=== Genome annotations files ===</strong> <strong><em>Solanum lycopersicum </em>Heinz1706</strong> <strong>ITAG2.4</strong> Gene File Format (GFF): ITAG2.4_gene_models.gff Gene Transfer Format (GTF): ITAG2.4_gene_models.gtf <strong>ITAG4.0</strong> Gene File Format (GFF): ITAG4.0_gene_models.gff General Transfer Format (GTF): ITAG4.0_gene_models.gtf MapMan annotation: S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv was obtained with Mercator 3.6 using the ITAG4.0_proteins.fasta file. <strong><em>Solanum lycopersicoides </em>LA2951</strong> Gene File Format: S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 <strong><em>Solanum habrochaites </em>PI127826</strong> (Based on the 2018 Hotel Project assembly): a GFF file was produced using RepeatMasker and funannotate and is named Solanum_habrochaites_PI127826.gff3. The companion script with the performed steps is available in this data record as well and is called S_habrochaites_PI127826_funannotate_steps.sh (Based on the 2021 Dovetails Genomic project): Solanum_habrochaites_PI127826_gene_models.gff <strong>Additional information:</strong> 2021 Dovetails Genomics complete <strong>assembly</strong> project report<strong>: </strong>dovetails_genomics_2021.tar.gz 2021 Dovetails Genomics complete <strong>annotation </strong>project report: dovetails_genomics_annotation_report_2021.tar.gz <strong>Reference:</strong> 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 (<em>Solanum</em> section <em>Lycopersicon</em>) clade by whole‐genome sequencing. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616 Stam et al. 2019. The <em>de Novo</em> Reference Genome and Transcriptome Assemblies of the Wild Tomato Species <em>Solanum chilense</em> Highlights Birth and Death of NLR Genes Between Tomato Species. G3: Genes, Genomes, Genetics December 1, 2019 vol. 9 no. 12 3933-3941; https://doi.org/10.1534/g3.119.400529