DOI: 10.5281/zenodo.3952453
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> (assemblies 3.0 and 4.0): 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 (technology hotel project 2018): PI127826.final.fasta <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>Solanum lycopersicum (assembly</em> 4.0): Transcriptome: ITAG4.0_cDNA.fasta Proteome: ITAG4.0_proteins.fasta <em>Solanum pennellii </em>(one version only from Bolger et al., 2014): Transcriptome: Spenn-v2-cds-annot.fa Solanum lycopersicoides (version 1.0) Transcriptome: S_lycopersicoides_LA2951_v1.0_cds.fasta Proteome: S_lycopersicoides_LA2951_v1.0_proteins.fasta <strong>Genome annotations files</strong> <em>Solanum lycopersicum</em> Gene File Format: ITAG4.0_gene_models.gff 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. <em>Solanum lycopersicoides:</em> Gene File Format: S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 <br> <em>Solanum habrochaites</em> PI127826: a GFF file was produced using RepeatMasker (see below) and Braker. <pre><code class="language-bash">RepeatMasker -qq -e rmblast -small -xsmall -pa 10 -lib mipsREdat_9.3p_Eudicot_TEs.fasta -dir repeat_masking_run/ PI127826.fasta</code></pre> LA1777 <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