Evaluation of Wild Tomato Accessions (Solanum Spp.)
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Genome Skimming for Phylogenomics
Genome skimming for phylogenomics Steven Andrew Dodsworth School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy November 2015 1 Statement of originality I, Steven Andrew Dodsworth, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged and my contribution indicated. Previously published material is also acknowledged and a full list of publications is given in the Appendix. Details of collaboration and publications are given at the start of each chapter, as appropriate. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: 16th November 2015 2 Frontispiece: Nicotiana burbidgeae Symon at Dalhousie Springs, South Australia. 2014. Photo: S. Dodsworth. 3 Acknowledgements Firstly, I would like to thank my PhD supervisors, Professor Andrew Leitch and Professor Mark Chase. -
DNA Variation in a Diversity Panel of Tomato Genetic Resources
J. AMER.SOC.HORT.SCI. 146(5):339–345. 2021. https://doi.org/10.21273/JASHS05066-21 DNA Variation in a Diversity Panel of Tomato Genetic Resources Joanne A. Labate Plant Genetic Resources Unit, Agricultural Research Service, U.S. Department of Agriculture, 630 W. North St., Geneva, NY 14456 ADDITIONAL INDEX WORDS. genotyping by sequencing, germplasm, Plant Variety Protection, single nucleotide polymorphism, Solanum lycopersicum, Solanum pimpinellifolium ABSTRACT. A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum) acces- sions was genotyped using genotyping by sequencing. These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable cultivar San Marzano. Most of the 34,531 discovered single nucleotide polymorphisms were rare and therefore excluded from downstream analyses. A total of 3713 high-quality, mapped single nucleotide polymorphisms that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these phenotypically and geographically diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement. Vegetable producers require an abundance of genetic diver- for purposes of breeding, research, and higher education. -
An Integrated Analytical Approach Reveals Trichome 3 Acylsugar Metabolite Diversity in the Wild Tomato 4 Solanum Pennellii
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 31 August 2020 doi:10.20944/preprints202008.0702.v1 1 Article 2 An Integrated Analytical Approach Reveals Trichome 3 Acylsugar Metabolite Diversity in the Wild Tomato 4 Solanum Pennellii 5 Daniel B. Lybrand 1, Thilani M. Anthony 1, A. Daniel Jones 1 and Robert L. Last 1,2,* 6 1 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; 7 [email protected] (D.B.L); [email protected] (T.M.A); [email protected] (A.D.J) 8 2 Department of Plant Biology, Michigan State University, East Lansing, MI, USA 9 * Correspondence: [email protected] 10 Abstract: Acylsugars constitute an abundant class of pest- and pathogen-protective Solanaceae 11 family plant specialized metabolites produced in secretory glandular trichomes. Solanum pennellii 12 produces copious triacylated sucrose and glucose esters, and the core biosynthetic pathway 13 producing these compounds was previously characterized. We performed untargeted 14 metabolomic analysis of S. pennellii surface metabolites from accessions spanning the species range, 15 which indicated geographic trends in acylsugar profile and revealed two compound classes 16 previously undescribed from this species, tetraacylglucoses and flavonoid aglycones. A 17 combination of ultrahigh performance liquid chromatography high resolution mass spectrometry 18 (UHPLC-HR-MS) and NMR spectroscopy identified variations in number, length, and branching 19 pattern of acyl chains, and the proportion of sugar cores in acylsugars among accessions. The new 20 dimensions of acylsugar variation revealed by this analysis further indicate variation in the 21 biosynthetic and degradative pathways responsible for acylsugar accumulation. -
Differential and Synergistic Functionality of Acylsugars in Suppressing Oviposition by Insect Herbivores
RESEARCH ARTICLE Differential and Synergistic Functionality of Acylsugars in Suppressing Oviposition by Insect Herbivores Brian M. Leckie1☯¤, Damon A. D'Ambrosio2☯, Thomas M. Chappell2, Rayko Halitschke3, Darlene M. De Jong1, André Kessler3, George G. Kennedy2, Martha A. Mutschler1* 1 Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America, 2 Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America, 3 Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America a11111 ☯ These authors contributed equally to this work. ¤ Current address: School of Agriculture, Tennessee Technological University, Cookeville, Tennessee, United States of America * [email protected] OPEN ACCESS Abstract Citation: Leckie BM, D'Ambrosio DA, Chappell TM, Acylsugars are secondary metabolites exuded from type IV glandular trichomes that pro- Halitschke R, De Jong DM, Kessler A, et al. (2016) Differential and Synergistic Functionality of vide broad-spectrum insect suppression for Solanum pennellii Correll, a wild relative of culti- Acylsugars in Suppressing Oviposition by Insect vated tomato. Acylsugars produced by different S. pennellii accessions vary by sugar Herbivores. PLoS ONE 11(4): e0153345. moieties (glucose or sucrose) and fatty acid side chains (lengths and branching patterns). doi:10.1371/journal.pone.0153345 Our objective was to determine which acylsugar compositions more effectively suppressed Editor: Xiao-Wei Wang, Zhejiang University, CHINA oviposition of the whitefly Bemisia tabaci (Gennadius) (Middle East—Asia Minor 1 Group), Received: August 6, 2015 tobacco thrips, Frankliniella fusca (Hinds), and western flower thrips, Frankliniella occidenta- Accepted: March 28, 2016 lis (Pergande). -
Inflorescence Development in Two Tomato Species
111 NOTE / NOTE Inflorescence development in two tomato species N. Welty, C. Radovich, T. Meulia, and E. van der Knaap Abstract: The inflorescence of tomato has been characterized as either a cyme or raceme. Cymose inflorescences are de- terminate, whereas racemose inflorescences are indeterminate. In this study, we addressed the discrepancy in inflorescence architecture by analyzing the morphology of a wild relative of tomato Solanum pimpinellifolium L. and four domesticated Solanum lycopersicum L. lines. Careful observation of developing inflorescences of both species showed a bifurcation of the meristem into a determinate floral and an indeterminate inflorescence meristem. Interestingly, higher fruit carpel num- ber was associated with delayed floral development, which might give the impression of determinate growth in some of the lines. Nevertheless, our results demonstrated that tomato inflorescences are indeterminate in nature regardless of the line studied. Floral buds were formed concomitantly with the development of the inflorescence meristem and not on the flanks of the peduncle, a characteristic of racemose growth. Thus, tomato inflorescences should be classified as a cyme with the note that the inflorescence meristem does not terminate into a flower and, in fact, maintains indeterminacy. In ad- dition, S. pimpinellifolium produced many more flowers in a highly regular manner when compared with the cultivated types. This demonstrated the usefulness of wild relatives of tomato as a tool to further understand flower and fruit devel- opment in this crop species. Key words: inflorescence, tomato, cyme, raceme, meristem, bifurcation. Re´sume´ : On a caracte´rise´ l’inflorescence de la tomate comme une cyme ou un race`me. -
Acylsugars Protect Nicotiana Benthamiana Against Insect Herbivory and Desiccation
Acylsugars Protect Nicotiana Benthamiana Against Insect Herbivory and Desiccation Honglin Feng Boyce Thompson Institute for Plant Research Lucia Acosta-Gamboa Cornell University Lars H Kruse Cornell University Jake D Tracy Cornell University Seung Ho Chung Boyce Thompson Institute for Plant Research Alba Ruth Nava Fereira The University of Texas at San Antonio Sara Shakir Boyce Thompson Institute for Plant Research Hongxing Xu Boyce Thompson Institute for Plant Research Garry Sunter The University of Texas at San Antonio Michael A Gore Cornell University Clare L Casteel Cornell University Gaurav D. Moghe Cornell University Georg Jander ( [email protected] ) Boyce Thompson Institute For Plant Research https://orcid.org/0000-0002-9675-934X Research Article Keywords: acylsugar, aphid, ASAT, desiccation, Nicotiana benthamiana, whitey Posted Date: June 15th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-596878/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Article Title 2 Acylsugars protect Nicotiana benthamiana against insect herbivory and desiccation 3 4 5 Author names 6 Honglin Fenga, Lucia Acosta-Gamboab, Lars H. Krusec,f, Jake D. Tracyd,g, Seung Ho Chunga, Alba Ruth 7 Nava Fereirae, Sara Shakira,h, Hongxing Xua,i, Garry Suntere, Michael A. Goreb, Clare L. Casteeld, Gaurav 8 D. Moghec, Georg Jandera* 9 10 11 Author Affiliations 12 aBoyce Thompson Institute, Ithaca NY, USA 13 bPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, -
Open Ohlsondissertation.Pdf
The Pennsylvania State University The Graduate School Intercollege Graduate Degree Program in Genetics GENETIC CHARACTERIZATION AND MAPPING OF LATE BLIGHT RESISTANCE GENES IN THE WILD TOMATO ACCESSIONS PI 163245 AND PI 224710 A Dissertation in Genetics by Erik William Ohlson © 2015 Erik William Ohlson Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2015 ii The dissertation of Erik William Ohlson was reviewed and approved* by the following: Majid R. Foolad Professor of Plant Genetics Dissertation Advisor David R. Huff Professor of Turfgrass Breeding and Genetics Chair of Committee Surinder Chopra Professor of Maize Genetics Beth K. Gugino Associate Professor of Vegetable Pathology Timothy W. McNellis Associate Professor of Plant Pathology Yinong Yang Associate Professor of Plant Pathology Robert F. Paulson Professor of Veterinary and Biomedical Sciences Chair of the Intercollege Graduate Degree Program in Genetics *Signatures are on file in the Graduate School. iii ABSTRACT Late blight (LB), caused by the oomycete Phytophthora infestans (Mont.) de Bary is one of the most destructive diseases of tomato and potato worldwide. Development of fungicide resistant and more aggressive P. infestans clonal lineages has emphasized the importance of discovering and incorporating new genetic resistance in tomato cultivars. Although the cultivated tomato, Solanum lycopersicum L., contains limited genetic diversity, several related wild species of tomato are suitable for identification of new desirable traits. Previously, 67 S. pimpinellifolium accessions were screened for LB resistance in field, greenhouse and detached leaflet trials and 12 accessions with strong resistance to LB were identified. In this dissertation, two resistant accessions, PI 163245 and PI 224710, were selected for further genetic characterization. -
Evolutionary Routes to Biochemical Innovation Revealed by Integrative
RESEARCH ARTICLE Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway Gaurav D Moghe1†, Bryan J Leong1,2, Steven M Hurney1,3, A Daniel Jones1,3, Robert L Last1,2* 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States; 2Department of Plant Biology, Michigan State University, East Lansing, United States; 3Department of Chemistry, Michigan State University, East Lansing, United States Abstract The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome- localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of *For correspondence: [email protected] innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the † Present address: Section of emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non- Plant Biology, School of model plant species that remain underexplored. Integrative Plant Sciences, DOI: https://doi.org/10.7554/eLife.28468.001 Cornell University, Ithaca, United States Competing interests: The authors declare that no Introduction competing interests exist. -
Variations of Secondary Metabolites Among Natural Populations of Sub
Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility Bastien Labarrere, Andreas Prinzing, Thomas Dorey, Emeline Chesneau, Françoise Hennion To cite this version: Bastien Labarrere, Andreas Prinzing, Thomas Dorey, Emeline Chesneau, Françoise Hennion. Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility. Plants, MDPI, 2019, 8 (7), pp.234. 10.3390/plants8070234. hal-02192278v2 HAL Id: hal-02192278 https://hal.archives-ouvertes.fr/hal-02192278v2 Submitted on 24 Jul 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. plants Article Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility Bastien Labarrere 1, Andreas Prinzing 1, Thomas Dorey 2, Emeline Chesneau 1 and Françoise Hennion 1,* 1 UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France 2 Institut für Systematische und Evolutionäre Botanik, Zollikerstrasse 107, 8008 Zürich, Switzerland * Correspondence: [email protected] Received: 24 May 2019; Accepted: 16 July 2019; Published: 19 July 2019 Abstract: Plants produce a high diversity of metabolites which help them sustain environmental stresses and are involved in local adaptation. -
Solanum Section Lycopersicon: Solanaceae)
Biological Journal of the Linnean Society, 2016, 117, 96–105. With 4 figures. Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae) 1,2 2,3 € 4 5 STEVEN DODSWORTH *, MARK W. CHASE , TIINA SARKINEN , SANDRA KNAPP and ANDREW R. LEITCH1 1School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK 2Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK 3School of Plant Biology, The University of Western Australia, Crawley, WA, 6009, Australia 4Royal Botanic Garden, Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK 5Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK Received 17 February 2015; revised 7 May 2015; accepted for publication 21 May 2015 High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon)to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. -
Scientists' Tomato Genome-Mapping Project Provides Key to Unlocking
Scientists from the U.S. Agricultural Research Service (ARS) and the Boyce Thompson Institute (BTI) may have pinpointed a gene responsible for improved flavor profiles for tomatoes, thanks to their recent genome-mapping project. For the study, molecular biologist James Giovannoni with the ARS Plant, Soil and Nutrition Research Laboratory and BTI bioinformatics scientist Zhangjun Fei constructed the pan- genome for the cultivated tomato and its wild relatives, mapping almost 5,000 previously undocumented genes. A genome is a biological map of an organism's genes and their functions. But a genome is usually of a single variety, which then acts as a reference genome for the rest of the species. This pan-genome includes all of the genes from 725 different cultivated and closely related wild tomatoes, which revealed 4,873 genes that were absent from the original reference genome. While cultivated tomatoes have a wide range of physical and metabolic variation, there have been several extreme bottlenecks during its domestication and breeding. This means today's tomatoes have a narrow genetic base. The pan-genome helps identify what additional genes beyond the reference might be available for crop breeding and improvement. In modern times, breeders have concentrated on traits such as yield, shelf life, disease resistance and stress tolerance - traits that have been economically important to growers. "One of the most important discoveries from constructing this pan-genome is a rare form of a gene labeled TomLoxC, which mostly differs in the version of its DNA gene promoter. The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid (fat)-involved volatiles—compounds that evaporate easily and contribute to aroma," explained Giovannoni. -
The 12Th Solanaceae Conference
SOL2015 would like to thank our sponsors: The 12th Solanaceae Conference The 12th Solanaceae Conference 1 The 12th Solanaceae Conference 2 CONTENTS Scientific Committee, Conference Chairs and Speakers ..................................... 4 Map of the Conference Site ............................................................................... 5 Social Events ..................................................................................................... 6 Program at a Glance .......................................................................................... 9 Scientific Program ............................................................................................. 10 Abstract (Monday, October 26th) Keynote lecture (KL‐1) ...................................................................................... 23 Session I – Plant Growth & Development ........................................................ 24 Session II – Biodiversity .................................................................................... 27 Session III – Molecular Breeding ...................................................................... 30 Session IV – Bioinformatics and SGN Workshop .............................................. 32 Abstract (Tuesday, October 27th) Keynote lecture (KL‐2) ...................................................................................... 34 Session V – Flower, Fruit and Tuber Biology .................................................... 35 Abstract (Wednesday, October 28th) Keynote lecture (KL‐3)