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90 results for “lycopersicum”
Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum with TAP treatment
GEO Series GSE102581. Solanum lycopersicum. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Systematic identification of long non-coding RNAs under allelopathic interference of PHBA in S. lycopersicum
GEO Series GSE142733. Solanum lycopersicum. 9 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Stem trichome mRNA-Seq from lycopersicum x habrochaites crosses (Parents and F1)
<p><strong>Stem trichome mRNA-Seq datasets from different crossing materials.</strong></p> <p>Genetic material</p> <p>Obtained from ENZA Zaden. The pollen from <em>S. habrochaites</em> LA1777 or PI127826 was placed on the pistil of <em>S. lycopersicum to obtain </em>interspecific crosses. </p> <p>The pollen of <em>S. habrochaites</em> LA1777 was placed on the pistil of PI127826 to obtain <em>S. habrochaites</em> F1.</p> <p><strong>Sample collection</strong></p> <p>....</p> <p><strong>Total RNA isolation</strong></p> <p><strong>....</strong></p> <p><strong>Sequencing </strong></p> <p>...</p> <p>Sample table</p> <pre><code class="language-markdown">| sample | species | cross | |--------------------- |--------------------------------------- |---------- | | 14865_PI127826_F1 | S. lycopersicum x S. habrochaites | F1 | | LA1777_4 | S. habrochaites | Parent | | LA1777_F1_3 | S. lycopersicum x S. habrochaites | F1 | | LA1777_P1_Cv_4 | S. lycopersicum | Parent | | PI26_P1_cv_i | S. lycopersicum | Parent | | PI26_P2_w_4 | S. habrochaites f. hirsutum | Parent | | PI26xLA1777_F1_J | S. habrochaites | F1 |</code></pre> <p> </p>
Stem trichome mRNA-Seq from S. lycopersicum x S. habrochaites PI127826 crosses (F2 lines)
<p><strong>Stem trichome mRNA-Seq datasets from different crossing materials.</strong></p> <p>Genetic material</p> <p>Obtained from ENZA Zaden. The pollen from <em>S. habrochaites</em> PI127826 was placed on the pistil of <em>S. lycopersicum to obtain </em>interspecific crosses. </p> <p><strong>Sample collection</strong></p> <p>....</p> <p><strong>Total RNA isolation</strong></p> <p><strong>....</strong></p> <p><strong>Sequencing </strong></p> <p>...</p> <p><strong>Sample table</strong></p> <p>See the samples.csv file.</p> <p> </p>
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>
iSB09 and iCB elicit ABA-responsive gene expression in Solanum lycopersicum seedlings
GEO Series GSE256238. Solanum lycopersicum. 12 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptome analysis of responses to water deficit in Solanum lycopersicum and S. pimpinellifolium roots
GEO Series GSE39894. Solanum lycopersicum; Solanum pimpinellifolium. 46 samples. Type: Expression profiling by array.
The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium
GEO Series GSE62196. Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pimpinellifolium. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA-seq and messenger RNA-seq of F1 cross between different species of tomato (lycopersicum, habrochaites)
<p>Small RNA and messenger RNA data from stem trichomes of various crosses (S. lycopersicum x S. habrochaites or S. habrochaites with itself). </p> <p>There are now also R2 reads for the samples. Reason for this is that the Mid Output flow cell doesn’t have the 1x75 option.</p> <p>The sample list is available in F1_samples.csv</p>
Calcium treatment can delay tomato (Solanum lycopersicum L.) fruit senescence
GEO Series GSE73520. Solanum lycopersicum. 10 samples. Type: Expression profiling by high throughput sequencing.
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