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Genomic sequences and annotations for Solanum lycopersicum, Solanum pennellii and Solanum habrochaites

=== Genome sequences ===    These are the different genome references (fasta formats) available for: <ul> <li>Solanum lycopersicum: <ul> <li><a href="https://zenodo.org/api/files/c5778399-5188-4959-93b7-1738584c0f72/S_lycopersicum_chromosomes.2.50.fa.gz">S_lycopersicum_chromosomes.2.50.fa.gz</a></li> <li><a href="https://zenodo.org/api/files/94d37cf6-6e8b-47c8-96c7-b82ae363ccd7/S_lycopersicum_chromosomes.3.00.fa.tar.gz?versionId=04729276-a75e-4652-8cfe-07359b13bd8c">S_lycopersicum_chromosomes.3.00.fa.tar.gz</a></li> <li><a href="https://zenodo.org/api/files/57840fa9-db90-4795-af03-8dbd2f711b69/S_lycopersicum_chromosomes.4.00.fa.tar.gz?versionId=a006a20e-5a34-47c9-8f81-feb782f9e68d">S_lycopersicum_chromosomes.4.00.fa.tar.gz</a></li> </ul> </li> <li>Solanum pennellii (one version only from Bolger et al., 2014) :  <ul> <li><a href="https://zenodo.org/api/files/94d37cf6-6e8b-47c8-96c7-b82ae363ccd7/Spenn.fasta.tar.gz?versionId=18b34053-cb37-4e47-9025-5213b0455347">Spenn.fasta.tar.gz</a></li> </ul> </li> <li>Solanum habrochaites LA1777 (technology hotel project 2018): <ul> <li><a href="https://zenodo.org/api/files/94d37cf6-6e8b-47c8-96c7-b82ae363ccd7/LA1777.final.fasta">LA1777.final.fasta</a>  </li> </ul> </li> <li>Solanum habrochaites PI127826: <ul> <li>2018 Hotel Project: <a href="https://zenodo.org/api/files/aa27d9ec-6ab7-4582-a17c-be7dfb0952a4/PI127826.final.fasta?versionId=d9748404-5d79-4a7b-af63-8dfd792436a0">PI127826.final.fasta  </a></li> <li>2021 Dovetails assembly: <a href="https://zenodo.org/api/files/2b9490ff-031c-49d7-85e3-c57ba37ff21a/PI127826_hirise_assembly.fasta.gz">PI127826_hirise_assembly.fasta.gz</a><a href="https://zenodo.org/api/files/aa27d9ec-6ab7-4582-a17c-be7dfb0952a4/PI127826.final.fasta?versionId=d9748404-5d79-4a7b-af63-8dfd792436a0"> </a></li> </ul> </li> <li>Solanum habrochaites LYC4 (from the paper of <a href="https://pubmed.ncbi.nlm.nih.gov/25039268/">Aflitos et al. 2014</a>. 3rd assembly version): <ul> <li><a href="https://zenodo.org/api/files/77a91023-8321-4f8e-86a6-1ae3b8197edf/S_habrochaites_LYC4_genome_assembly_v3.0_scaffold_scarpa.fasta?versionId=71501782-d9a5-49c8-83ed-511ba7deb6fa">S_habrochaites_LYC4...</a></li> </ul> </li> <li>Solanum arcanum LA2172 (from the paper of <a href="https://pubmed.ncbi.nlm.nih.gov/25039268/">Aflitos et al. 2014</a>. 3rd assembly version): <ul> <li><a href="https://zenodo.org/api/files/179d217c-2a83-47ca-8180-3e4821b2481e/LA2172.fasta.tar.gz">LA2172.fasta.tar.gz</a></li> </ul> </li> <li>Solanum chilense LA3111 (from the paper of <a href="https://www.g3journal.org/content/9/12/3933">Stam et al. 2019</a>, NCBI assembly ASM601370v1): <ul> <li><a href="https://zenodo.org/api/files/179d217c-2a83-47ca-8180-3e4821b2481e/LA3111.fasta.tar.gz">LA3111.fasta.tar.gz</a></li> </ul> </li> <li>Solanum lycopersicoides LA2951 (from the work of The Boyce Thompson Institute and RWTH Aachen University: <a href="https://solgenomics.net/organism/Solanum_lycopersicoides/genome">link</a>): <ul> <li><a href="https://zenodo.org/api/files/77a91023-8321-4f8e-86a6-1ae3b8197edf/S_lycopersicoides_LA2951_v1.0_chromosomes_contigs.fasta.tar.gz">S_lycopersicoides_LA2951_v1.0_chromosomes.fasta.tar.gz</a></li> </ul> </li> </ul> 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.   === Transcriptomes and proteomes === <ul> <li>Solanum lycopersicum (assembly 4.0): <ul> <li>Transcriptome: <a href="https://zenodo.org/api/files/2a1ca78d-e799-4034-9abd-b760e4ea3694/ITAG4.0_cDNA.fasta?versionId=76df390e-af94-4ebb-b6a7-05cf2dca5010">ITAG4.0_cDNA.fasta</a> </li> <li>Proteome: <a href="https://zenodo.org/api/files/2a1ca78d-e799-4034-9abd-b760e4ea3694/ITAG4.0_proteins.fasta?versionId=cdc2eea1-f5be-4153-92d8-18a4cd77931c">ITAG4.0_proteins.fasta</a></li> </ul> </li> <li>Solanum pennellii (one version only from Bolger et al., 2014): <ul> <li>Transcriptome: <a href="https://zenodo.org/record/3885088/files/Spenn-v2-cds-annot.fa?download=1">Spenn-v2-cds-annot.fa</a></li> <li>Proteome: <a href="https://zenodo.org/api/files/2a1ca78d-e799-4034-9abd-b760e4ea3694/Spenn-v2-aa-annot.fa">Spenn-v2-aa-annot.fa</a></li> </ul> </li> <li>Solanum lycopersicoides (version 1.0) <ul> <li>Transcriptome: <a href="https://zenodo.org/api/files/77a91023-8321-4f8e-86a6-1ae3b8197edf/S_lycopersicoides_LA2951_v1.0_cds.fasta">S_lycopersicoides_LA2951_v1.0_cds.fasta </a></li> <li>Proteome: <a href="https://zenodo.org/api/files/77a91023-8321-4f8e-86a6-1ae3b8197edf/S_lycopersicoides_LA2951_v1.0_proteins.fasta">S_lycopersicoides_LA2951_v1.0_proteins.fasta </a></li> </ul> </li> <li>Solanum habrochaites PI127826 <ul> <li>Transcriptome: <a href="https://zenodo.org/api/files/7ba7db3d-f8dd-43f9-b990-c1a5d3487b8f/Solanum_habrochaites_PI127826_mRNAs.fasta">Solanum_habrochaites_PI12826_mRNAs.fasta</a> (2018 Hotel Project assembly)</li> <li>Transcriptome (2021 Dovetails): <a href="https://zenodo.org/api/files/13145d97-7394-4b89-83e6-039680fb8844/Solanum_habrochaites_PI127826_CDS_Dovetails_2021.fasta">Solanum_habrochaites_PI127826_CDS_Dovetails_2021.fasta </a></li> <li>Proteome (2021 Dovetails): <a href="https://zenodo.org/api/files/13145d97-7394-4b89-83e6-039680fb8844/Solanum_habrochaites_PI127826_protein_Dovetails_2021.fasta">Solanum_habrochaites_PI127826_protein_Dovetails_2021.fasta</a> </li> </ul> </li> </ul>   === Genome annotations files === Solanum lycopersicum Heinz1706 <ul> <li>ITAG2.4 <ul> <li>Gene File Format (GFF): <a href="https://zenodo.org/api/files/c5778399-5188-4959-93b7-1738584c0f72/ITAG2.4_gene_models.gff3">ITAG2.4_gene_models.gff </a></li> <li>Gene Transfer Format (GTF): <a href="https://zenodo.org/api/files/3e34c90f-9fce-4947-9ad3-0573572d942b/ITAG2.4_gene_models.gtf">ITAG2.4_gene_models.gtf</a></li> </ul> </li> <li>ITAG4.0 <ul> <li>Gene File Format (GFF): <a href="https://zenodo.org/api/files/5d1c61b1-e0b9-4351-8fd4-127edb9b8e08/ITAG4.0_gene_models.gff?versionId=f22ed8c3-6629-4d88-b6b7-472f3cd7c975">ITAG4.0_gene_models.gff</a></li> <li>General Transfer Format (GTF): <a href="https://zenodo.org/api/files/57840fa9-db90-4795-af03-8dbd2f711b69/ITAG4.0_gene_models.gtf">ITAG4.0_gene_models.gtf</a></li> <li>MapMan annotation: <a href="https://zenodo.org/api/files/5d1c61b1-e0b9-4351-8fd4-127edb9b8e08/S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv?versionId=bfa0b3d1-352a-470a-9504-c0f7611045f1">S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv</a> was obtained with Mercator 3.6 using the ITAG4.0_proteins.fasta file.</li> </ul> </li> </ul> Solanum lycopersicoides LA2951 <ul> <li>Gene File Format: <a href="https://zenodo.org/api/files/77a91023-8321-4f8e-86a6-1ae3b8197edf/S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3">S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 </a></li> </ul> Solanum habrochaites PI127826 <ul> <li>(Based on the 2018 Hotel Project assembly): a GFF file was produced using RepeatMasker and funannotate and is named<a href="https://zenodo.org/api/files/aa27d9ec-6ab7-4582-a17c-be7dfb0952a4/Solanum_habrochaites_PI127826.gff3?versionId=4bc7492e-2de1-4b67-a21c-bb04d2bc6c10"> Solanum_habrochaites_PI127826.gff3</a>. The companion script with the performed steps is available in this data record as well and is called <a href="https://zenodo.org/api/files/aa27d9ec-6ab7-4582-a17c-be7dfb0952a4/S_habrochaites_PI127826_funannotate_steps.sh">S_habrochaites_PI127826_funannotate_steps.sh</a></li> <li>(Based on the 2021 Dovetails Genomic project): <a href="https://zenodo.org/api/files/13145d97-7394-4b89-83e6-039680fb8844/Solanum_habrochaites_PI127826_gene_models.gff">Solanum_habrochaites_PI127826_gene_models.gff</a></li> </ul> Additional information: <ul> <li>2021 Dovetails Genomics complete assembly project report: <a href="https://zenodo.org/api/files/2b9490ff-031c-49d7-85e3-c57ba37ff21a/dovetails_genomics_2021.tar.gz">dovetails_genomics_2021.tar.gz </a></li> <li>2021 Dovetails Genomics complete annotation project report:  <a href="https://zenodo.org/api/files/13145d97-7394-4b89-83e6-039680fb8844/dovetails_genomics_annotation_report_2021.tar.gz">dovetails_genomics_annotation_report_2021.tar.gz</a></li> </ul> 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. <a href="https://www.biorxiv.org/content/10.1101/767764v1">https://www.biorxiv.org/content/10.1101/767764v1</a> Aflitos et al. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing. <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616">https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616</a> Stam et al. 2019. The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species. G3: Genes, Genomes, Genetics December 1, 2019 vol. 9 no. 12 3933-3941; <a href="https://doi.org/10.1534/g3.119.400529">https://doi.org/10.1534/g3.119.400529 </a>

ShareScore

16/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 0
Reuse readiness: 0
Engagement: 4

Topics

tomato pennellii genome LA1777 habrochaites PI127826 lycopersicum LYC4 LA0716