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7 results for “Solanum habrochaites”
Fig. 4 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior
Fig. 4. Effect of pure β-caryophyllene and α-humulene on M. euphorbiae feeding performance (A–C) and choice behavior (D). Different amounts of a mix of pure β-caryophyllene and α-humulene (3:1 ratio) were added to the feeding diet. The data in (A), (B), and (C) show the comparison of Kaplan-Meier survival curves (logrank test, α =0.05), gel saliva density (Tukey's HSD, α =0.05), and number of honeydew drops (ANOVA, α = 0.05), respectively, upon addition of different amounts of pure sesquiterpenes to the artificial diet. The data in (D) represent the behavioral responses of aphid alatae to odors from leaves of c.v. M82 alone (right bars) or from leaves of c.v. M82 leaves in combination with different amounts of a mix of pure β-caryophyllene and α-humulene (left bars) (Chi-square goodness of fit; *, P <0.05; **, P <0.01).
Fig. 5 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior
Fig. 5. α-Santalene and α-bergamotene producing tomato introgression line affects performance, feeding and choice behavior of M. euphorbiae. (A) Performance of M. euphorbiae apterae arrested on the leaf surface of S. lycopersicum LA4024, S. habrochaites LA1777, and the introgression lines LA3935, LA3934, LA3936, and LA3937. Values for longevity and fecundity are presented as mean ± SE and compared by Tukey's HSD test (α =0.05). (B) Kaplan-Meier estimates of survivorship of M. euphorbiae apterae feeding on artificial diets containing leaf dip extracts of S. lycopersicum LA4024, S. habrochaites LA1777, and the introgression line LA3935 (logrank test, α = 0.05). (C) and (D) Box plots represent means ± SE of gel saliva density (cm 2) and number of honeydew drops, respectively. Tukey's HSD tests (α = 0.05) are used for post-hoc analysis. (E) Choice of M. euphorbiae alatae between odors from LA4024 leaves alone (left bars) and from LA4024 leaves with added leaf dip extracts (100 and 300 μL) from the introgression line LA3935 or S. habrochaites LA1777 (right bars) (Chi-square goodness of fit; *, P <0.05; **, P <0.01).
Fig. 3 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior
Fig. 3. Choice behavior of M. euphorbiae alatae in an open Y-track olfactometer. (A) Choice of aphids between air and odors from leaves of different S. lycopersicum cultivars or S. habrochaites accessions. (B) Choice of aphids between odors from leaves of c.v. M82 and different S. habrochaites accessions. (C) Choice of aphids between odors from leaves of c.v. M82 leaves alone (left bars) and from leaves of c.v. M82 leaves with added S. habrochaites leaf dip extracts (right bars). Asterisks following each pair of bars indicates significant differences according to Chi-square goodness of fit (⋅, P <0.07; *, P <0.05; **, P <0.01).
Fig. 2 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior
Fig. 2. Feeding performance of M. euphorbiae apterae on artificial diets containing leaf dip extracts of S. lycopersicum c.v. M82 and different S. habrochaites accessions (MTBE solvent control). (A) Kaplan-Meier estimates of survivorship and analysis of log-rank test (α =0.05). (B) Box and violin plots represent mean ± SE of gel saliva density (cm 2) and the probability density, respectively. (C) Number of honeydew drops accumulated in the feeding chambers. Asterisks in (B) and (C) represent significant differences between diets with leaf dip extracts and control based on Dunnett's test (⋅, P <0.08; *, P <0.05; **, P <0.01; ***, P <0.001).
Fig. 1 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior
Fig. 1. Longevity (A) and fecundity (B) of M. euphorbiae apterae arrested on the leaf surface of two S. lycopersicum cultivars and different S. habrochaites accessions. Solanum habrochaites accessions represent five chemotypes characterized by the production of different sesquiterpenes in their glandular trichomes. Values for longevity and fecundity are presented as mean ± SE. Different letters indicate that logarithmic values were significantly different (Tukey's HSD test, α = 0.05).
DNA-seq of Solanum habrochaites PI127826 and LA1777 DNA (part II)
<p>Illumina paired-end HiSeqX reads from the genomic DNA isolated from young leaves of three plants from <em>S. habrochaites</em>:</p> <ol> <li>Solanum habrochaites PI127826</li> <li>Solanum habrochaites LA1777 (wild-type)</li> <li>Solanum habrochaites LA1777 X-ray mutated to allow self-compatibility</li> </ol> <p><em>Nota bene:</em></p> <p>This is the second part of the data record.</p> <p>The first part of the data record is available at: <a href="https://doi.org/10.5281/zenodo.3987917">https://doi.org/10.5281/zenodo.3987917</a></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>
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