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6 results for “Solanum pennellii”
Data from: Solanum pennellii (LA5240) backcross inbred lines (BILs) for high resolution mapping in tomato
<p>Wild species are an invaluable source of new traits for crop improvement. Over the years the tomato community bred cultivated lines that carry introgressions from different species of the tomato tribe to facilitate trait discovery and mapping. The next phase in such projects is to find the genes that drive the identified phenotypes. This can be achieved by genotyping a few thousand individuals resulting in fine-mapping that can potentially identify the causative gene. To couple trait discovery and fine mapping we are presenting large, recombination-rich, Backcross Inbred Line (BIL) populations involving an unexplored accession of the wild, green-fruited species Solanum pennellii (LA5240; the Lost Accession) with two modern tomato inbreds: LEA, determinate, and TOP indeterminate. The LEA and TOP BILs are in BC2F6-8 generation and include 1,400 and 500 lines respectively. The BILs were genotyped with ~5,000 SPET markers, showing that in the euchromatic regions there was one recombinant every 17-18 Kb while in the heterochromatin a recombinant every 600-700 Kb (TOP and LEA respectively). To gain perspective on the topography of recombination we compared five independent members of the self-pruning gene family with their respective neighboring genes; based on PCR markers, in all cases we found recombinants. Further mapping analysis of two known morphological mutations that segregated in the BILs (Self-pruning and Hair), showed that the maximal delimited intervals were 73 Kb and 210 Kb respectively and included the known causative genes. The LOST_BILs provide a solid framework to study traits derived from a tolerant wild tomato.</p>
Data from: Solanum pennellii (LA5240) backcross inbred lines (BILs) for high resolution mapping in tomato
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Multiscale gene expression profiling of 1 cm root tips of control and submerged Oryza sativa, Medicago truncatula, Solanum lycopersicum and Solanum pennellii seedlings
GEO Series GSE128680. Solanum lycopersicum; Medicago truncatula; Oryza sativa Japonica Group; Solanum pennellii. 231 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
RNA-seq of Solanum lycopersicum cv. M82 and S. pennellii introgression line 3-5 day old root tip tissue
GEO Series GSE87162. Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii; Solanum pennellii. 305 samples. Type: Expression profiling by high throughput sequencing.
Expression data from leaflets of domesticated tomato and wild-related Solanum pennellii plants subjected to water stress
GEO Series GSE97045. Solanum lycopersicum; Solanum pennellii. 12 samples. Type: Expression profiling by array.
Genomic sequences and annotations for Solanum lycopersicum, Solanum pennellii and Solanum habrochaites
<p><strong>=== Genome sequences === </strong></p> <p> </p> <p>These are the different genome references (fasta formats) available for:</p> <ul> <li><em>Solanum lycopersicum</em>: <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><em>Solanum pennellii </em>(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><em>Solanum habrochaites</em> 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><em>Solanum habrochaites</em> 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><em>Solanum</em> <em>habrochaites</em> 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><em>Solanum arcanum</em> 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><em>Solanum chilense</em> 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><em>Solanum lycopersicoides</em> 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> <p>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.</p> <p> </p> <p><strong>=== Transcriptomes and proteomes ===</strong></p> <ul> <li><em><strong>Solanum lycopersicum</strong> (assembly</em> 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><em><strong>Solanum pennellii</strong> </em>(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><strong><em>Solanum lycopersicoides</em></strong> (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><strong><em>Solanum habrochaites </em>PI127826 </strong> <ul> <li><strong>Transcriptome: </strong><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><strong>Transcriptome (2021 Dovetails): </strong><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><strong>Proteome (2021 Dovetails): </strong><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><strong> </strong></li> </ul> </li> </ul> <p> </p> <p><strong>=== Genome annotations files ===</strong></p> <p><strong><em>Solanum lycopersicum </em>Heinz1706</strong></p> <ul> <li><strong>ITAG2.4</strong> <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><strong>ITAG4.0</strong> <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> <p><strong><em>Solanum lycopersicoides </em>LA2951</strong></p> <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> <p><strong><em>Solanum habrochaites </em>PI127826</strong></p> <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> <p><strong>Additional information:</strong></p> <ul> <li>2021 Dovetails Genomics complete <strong>assembly</strong> project report<strong>: </strong><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 <strong>annotation </strong>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> <p><strong>Reference:</strong></p> <p>Tomato Genome Sequencing Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature volume 485, pages 635–641.</p> <p>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 </p> <p>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></p> <p>Aflitos et al. 2014. Exploring genetic variation in the tomato (<em>Solanum</em> section <em>Lycopersicon</em>) 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></p> <p>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; <a href="https://doi.org/10.1534/g3.119.400529">https://doi.org/10.1534/g3.119.400529 </a></p> <p> </p> <p> </p>
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