DOCSLIB.ORG

Regulation of Monocot and Dicot Plant Development with Constitutively Active Alleles of Phytochrome B

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Regulation of Monocot and Dicot Plant Development with Constitutively Active Alleles of Phytochrome B UC Davis UC Davis Previously Published Works Title Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B. Permalink https://escholarship.org/uc/item/2p11v031 Journal Plant direct, 4(4) ISSN 2475-4455 Authors Hu, Wei Figueroa-Balderas, Rosa Chi-Ham, Cecilia et al. Publication Date 2020-04-27 DOI 10.1002/pld3.210 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Received: 3 December 2019 | Revised: 3 February 2020 | Accepted: 25 February 2020 DOI: 10.1002/pld3.210 ORIGINAL RESEARCH Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B Wei Hu1 | Rosa Figueroa-Balderas2,3 | Cecilia Chi-Ham2 | J. Clark Lagarias1 1Department of Molecular and Cellular Biology, University of California, Davis, CA, Abstract USA The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H 2 Public Intellectual Property Resource for or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active Agriculture (PIPRA), University of California, Davis, CA, USA conformation capable of sustaining photomorphogenesis in darkness. Here, we show 3Department of Viticulture and Enology, that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H) also encodes University of California, Davis, CA, USA a dominant “constitutively active” photoreceptor through comparative phenotypic Correspondence analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis Wei Hu, Department of Molecular and Cellular Biology, University of California, thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum Davis, CA 95616, USA. cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Email: [email protected] Brachypodium distachyon. Reciprocal transformation experiments show that the gain- Funding information of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are This work was supported by grants to J.C.L. from the National Institutes of Health stronger in host plants within the same class than across classes. Our studies also (NIGMS GM068552), the National Science reveal additional YHB-dependent traits in adult plants, which include extreme shade Foundation (IOS-1239577), and the USDA National Institute of Food and Agriculture tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced (CA-D*-MCB-4126-H). The contents of this tillering, and even viviparous seed germination. However, the strength of these gain- report are solely the responsibility of the authors and do not necessarily represent the of-function phenotypes depends on the specific combination of YHB allele and spe- official views of the NIH, NSF, or USDA. cies/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differ- ences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles. KEYWORDS flowering regulation, light signal transduction, photobiology, photoperiodism, phytochrome, shade avoidance This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. © 2020 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd. Plant Direct. 2020;4:1–19. wileyonlinelibrary.com/journal/pld3 | 1 2 | HU ET AL. 1 | INTRODUCTION can flower early in non-inductive photoperiods (Bagnall et al., 1995; Hajdu et al., 2015; Krall & Reed, 2000; Oka et al., 2004; Song et al., Plants possess an array of photoreceptors that mediate real-time 2015; Wallerstein, Wallerstein, Libman, Machnic, & Whitelam, 2002; light acclimation responses to optimize light capture and energy Wu, Zhang, Li, & Fu, 2011; Zhang, Stankey, & Vierstra, 2013), late resource allocation. Among the best studied of these sensors are in inductive and non-inductive photoperiods (Bagnall & King, 2001; the phytochromes, which mainly monitor red (R) and far-red (FR) Halliday, Thomas, & Whitelam, 1997; Hwang et al., 2014; Song et al., light fluences informing growth and developmental decisions that 2015), at the same time as WT (Endo, Nakamura, Araki, Mochizuki, primarily impact competition with neighboring plants (Ballare & & Nagatani, 2005; Palagyi et al., 2010; Schittenhelm, Menge- Pierik, 2017; Casal, 2013; de Wit, Galvao, & Fankhauser, 2016). Hartmann, & Oldenburg, 2004; Thiele, Herold, Lenk, Quail, & Gatz, Phytochromes sense visible light using a linear tetrapyrrole (bilin) 1999; Usami, Matsushita, Oka, Mochizuki, & Nagatani, 2007; Zheng, chromophore that is covalently linked to a conserved cysteine res- Yang, Jang, & Metzger, 2001), and even exhibit novel phenotypes idue in a multidomain apoprotein (Anders & Essen, 2015; Burgie & inconsistent with SAR suppression (Viczian, Klose, Adam, & Nagy, Vierstra, 2014; Rockwell, Su, & Lagarias, 2006). Plant PHY apopro- 2017). teins comprise an N-terminal photosensory “light input” module con- These observations underscore our incomplete understanding sisting of highly conserved PAS, GAF, and PHY domains, and a more of phyB's regulatory roles in plants and also challenge the tacit as- diverged C-terminal regulatory “signal output” module with two PAS sumption from model systems that these roles will be conserved in domains and a histidine kinase-related domain (HKRD) (Nagatani, all plant species. It is well established that phyB signaling requires 2010). Photoisomerization of the C15 double bond of the bilin chro- formation of stable and transient complexes with transcription mophore initiates the reversible interconversion between the inac- regulators, components of the proteasome, and factors that affect tive R-absorbing Pr form and the active FR-absorbing Pfr form of the circadian clock (Bae & Choi, 2008; Viczian et al., 2017; Wang & holophytochromes (phys), triggering structural changes throughout Wang, 2014). PhyB also can form heterodimers with other phys, that the polypeptide that are recognized by downstream signaling effec- is, with phyC-E in Arabidopsis (Clack et al., 2009; Sharrock & Clack, tors (Bae & Choi, 2008; von Horsten et al., 2016; Pham, Kathare, & 2004). Hence, the relative abundances of phyB homodimers and Huq, 2018). these heterodimeric species change when phyB levels are altered. As master regulators of plant growth and development, phys The regulatory behavior is even more complicated when phyB from influence seed germination, vegetative growth, photoperiodic flow- one plant species is expressed in another, since the affinity of the ering, storage organ development, photosynthesis, senescence, introduced phyB with endogenous phys and/or with other down- shade avoidance responses (SARs), and phase/amplitude of the stream signaling components cannot be assumed to be the same as circadian clock (Demotes-Mainard et al., 2016; Franklin & Quail, that occurring in the host. While this complexity accounts for the 2010). For this reason, phys have been a target of crop improve- difficulty to predict the phenotypic consequences of phyB expres- ment efforts for over three decades (Keller, Shanklin, Vierstra, & sion, it also implicates the potential of tailored phyB expression to Hershey, 1989; Smith, 1992; Smith, Casal, & Jackson, 1990). Three modify selective aspects of light-mediated development of crop major PHY lineages are present in flowering plant genomes, PHYA, plants without affecting others. PHYB, and PHYC, with gene expansion and/or loss having occurred Here, we exploited YHB alleles of rice (Oryza sativum) and in some eudicot species (Alba, Kelmenson, Cordonnier-Pratt, & Arabidopsis PHYB, the latter of which has been proven to be Pratt, 2000; Clack, Mathews, & Sharrock, 1994; Karve et al., 2012; constitutively active regardless of the light conditions (Hu, Su, & Mathews, 2010; Sheehan, Farmer, & Brutnell, 2004; Takano et al., Lagarias, 2009; Su & Lagarias, 2007). We reasoned that, as domi- 2005). Transgenic phytochrome-based crop improvement efforts nant alleles, YHBs could be used to suppress SARs in any plant cul- have predominantly exploited PHYA overexpression because, unlike tivar to mitigate deleterious consequences on crop performance phyB, phyA remains active in FR-enriched shade light (Ganesan, Lee, at high planting densities. Our studies examined the phenotypic Kim, & Song, 2017). SARs that include rapid internode elongation, consequences of heterologous expression of AtYHB in three eu- enhanced apical dominance, reduced photosynthesis efficiency, dicot species, tomato (Solanum lycopersicum) and two Nicotiana premature flowering and increased susceptibility to pathogen in- species (N. tabacum and N. sylvestris), and in the monocot species fection, reduce crop yields as plant density is increased (Carriedo, rice. Homologous OsPHYB- and OsYHB-expressing rice lines were Maloof, & Brady, 2016). Triggered when phyB is inactivated by FR constructed for comprehensive
Load more

Recommended publications
  • Appendix Color Plates of Solanales Species
    Appendix Color Plates of Solanales Species The first half of the color plates (Plates 1–8) shows a selection of phytochemically prominent solanaceous species, the second half (Plates 9–16) a selection of convol- vulaceous counterparts. The scientific name of the species in bold (for authorities see text and tables) may be followed (in brackets) by a frequently used though invalid synonym and/or a common name if existent. The next information refers to the habitus, origin/natural distribution, and – if applicable – cultivation. If more than one photograph is shown for a certain species there will be explanations for each of them. Finally, section numbers of the phytochemical Chapters 3–8 are given, where the respective species are discussed. The individually combined occurrence of sec- ondary metabolites from different structural classes characterizes every species. However, it has to be remembered that a small number of citations does not neces- sarily indicate a poorer secondary metabolism in a respective species compared with others; this may just be due to less studies being carried out. Solanaceae Plate 1a Anthocercis littorea (yellow tailflower): erect or rarely sprawling shrub (to 3 m); W- and SW-Australia; Sects. 3.1 / 3.4 Plate 1b, c Atropa belladonna (deadly nightshade): erect herbaceous perennial plant (to 1.5 m); Europe to central Asia (naturalized: N-USA; cultivated as a medicinal plant); b fruiting twig; c flowers, unripe (green) and ripe (black) berries; Sects. 3.1 / 3.3.2 / 3.4 / 3.5 / 6.5.2 / 7.5.1 / 7.7.2 / 7.7.4.3 Plate 1d Brugmansia versicolor (angel’s trumpet): shrub or small tree (to 5 m); tropical parts of Ecuador west of the Andes (cultivated as an ornamental in tropical and subtropical regions); Sect.
    [Show full text]
  • Fragrant Annuals Fragrant Annuals
    TheThe AmericanAmerican GARDENERGARDENER® TheThe MagazineMagazine ofof thethe AAmericanmerican HorticulturalHorticultural SocietySociety JanuaryJanuary // FebruaryFebruary 20112011 New Plants for 2011 Unusual Trees with Garden Potential The AHS’s River Farm: A Center of Horticulture Fragrant Annuals Legacies assume many forms hether making estate plans, considering W year-end giving, honoring a loved one or planting a tree, the legacies of tomorrow are created today. Please remember the American Horticultural Society when making your estate and charitable giving plans. Together we can leave a legacy of a greener, healthier, more beautiful America. For more information on including the AHS in your estate planning and charitable giving, or to make a gift to honor or remember a loved one, please contact Courtney Capstack at (703) 768-5700 ext. 127. Making America a Nation of Gardeners, a Land of Gardens contents Volume 90, Number 1 . January / February 2011 FEATURES DEPARTMENTS 5 NOTES FROM RIVER FARM 6 MEMBERS’ FORUM 8 NEWS FROM THE AHS 2011 Seed Exchange catalog online for AHS members, new AHS Travel Study Program destinations, AHS forms partnership with Northeast garden symposium, registration open for 10th annual America in Bloom Contest, 2011 EPCOT International Flower & Garden Festival, Colonial Williamsburg Garden Symposium, TGOA-MGCA garden photography competition opens. 40 GARDEN SOLUTIONS Plant expert Scott Aker offers a holistic approach to solving common problems. 42 HOMEGROWN HARVEST page 28 Easy-to-grow parsley. 44 GARDENER’S NOTEBOOK Enlightened ways to NEW PLANTS FOR 2011 BY JANE BERGER 12 control powdery mildew, Edible, compact, upright, and colorful are the themes of this beating bugs with plant year’s new plant introductions.
    [Show full text]
  • Wild Tobacco Genomes Reveal the Evolution of Nicotine Biosynthesis
    Wild tobacco genomes reveal the evolution of nicotine biosynthesis Shuqing Xua,1,2, Thomas Brockmöllera,1, Aura Navarro-Quezadab, Heiner Kuhlc, Klaus Gasea, Zhihao Linga, Wenwu Zhoua, Christoph Kreitzera,d, Mario Stankee, Haibao Tangf, Eric Lyonsg, Priyanka Pandeyh, Shree P. Pandeyi, Bernd Timmermannc, Emmanuel Gaquerelb,2, and Ian T. Baldwina,2 aDepartment of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; bCentre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany; cSequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; dInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria; eInstitute for Mathematics and Computer Science, Universität Greifswald, 17489 Greifswald, Germany; fCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China; gSchool of Plant Sciences, BIO5 Institute, CyVerse, University of Arizona, Tucson, AZ 85721; hNational Institute of Biomedical Genomics, Kalyani, 741251 West Bengal, India; and iDepartment of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, 700064 West Bengal, India Edited by Joseph R. Ecker, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, and approved April 27, 2017 (received for review January 4, 2017) Nicotine, the signature alkaloid of Nicotiana
    [Show full text]
  • Viewed Previously Was Constructed from SSR Markers Applied to a Mapping [31,32]
    Sierro et al. Genome Biology 2013, 14:R60 http://genomebiology.com/2013/14/6/R60 RESEARCH Open Access Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch and Nikolai V Ivanov* Abstract Background: Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species. Results: Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis. Conclusions: The reference genomes of N.
    [Show full text]
  • The Sequenced Angiosperm Genomes and Genome Databases
    REVIEW published: 13 April 2018 doi: 10.3389/fpls.2018.00418 The Sequenced Angiosperm Genomes and Genome Databases Fei Chen 1†, Wei Dong 1†, Jiawei Zhang 1, Xinyue Guo 1, Junhao Chen 2, Zhengjia Wang 2, Zhenguo Lin 3, Haibao Tang 1 and Liangsheng Zhang 1* 1 State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China, 2 State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China, 3 Department of Biology, Saint Louis University, St. Louis, MO, United States Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive Edited by: review for three major types of angiosperm genome databases, including databases Santosh Kumar Upadhyay, Panjab University, India for a single species, for a specific angiosperm clade, and for multiple angiosperm Reviewed by: species. The scope, tools, and data of each type of databases and their features Sumit Kumar Bag, are concisely discussed. The genome databases for a single species or a clade of National Botanical Research Institute species are especially popular for specific group of researchers, while a timely-updated (CSIR), India Xiyin Wang, comprehensive database is more powerful for address of major scientific mysteries at North China University of Science and the genome scale.
    [Show full text]
  • An Update of the Host Range of Tomato Spotted Wilt Virus Giuseppe Parrella, Patrick Gognalons, Kahsay Gebre Selassie, C
    An update of the host range of tomato spotted wilt virus Giuseppe Parrella, Patrick Gognalons, Kahsay Gebre Selassie, C. Vovlas, Georges Marchoux To cite this version: Giuseppe Parrella, Patrick Gognalons, Kahsay Gebre Selassie, C. Vovlas, Georges Marchoux. An update of the host range of tomato spotted wilt virus. Journal of Plant Pathology, Springer, 2003, 85 (4), pp.227-264. hal-02682821 HAL Id: hal-02682821 https://hal.inrae.fr/hal-02682821 Submitted on 1 Jun 2020 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. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License Journal of Plant Pathology (2003), 85 (4, Special issue), 227-264 Edizioni ETS Pisa, 2003 227 INVITED REVIEW AN UPDATE OF THE HOST RANGE OF TOMATO SPOTTED WILT VIRUS G. Parrella1, P. Gognalons2, K. Gebre-Selassiè2, C. Vovlas3 and G. Marchoux2 1 Istituto per la Protezione delle Piante del CNR, Sezione di Portici, Via Università 133, 80055 Portici (NA), Italy 2 Institute National de la Recherche Agronomique, Station de Pathologie Végétale, BP 94 - 84143 Montfavet Cedex, France 3 Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi and Istituto di Virologia Vegetale del CNR, Sezione di Bari, Via G.
    [Show full text]
  • ALKALOIDS in CERTAIN SPECIES and INTERSPECIFIC HYBRIDS of NICOTIANA» Although It Has Been Known for Many Years That the Main Al
    ALKALOIDS IN CERTAIN SPECIES AND INTERSPECIFIC HYBRIDS OF NICOTIANA» By HAROLD H. SMITH, assistant geneticist, Division of Tobacco Investigations, Bureau of Plant Industry, and CLAUDE R. SMITH, formerly chemist. Division of Insecticide Investigations, Bureau of Entomology and Plant Quarantine, Agri- cultural Research Administration^ United States Department of Agriculture INTRODUCTION Although it has been known for many years that the main alkaloid in the cultivated species Nicotiana tabacum L. and N. rustica L. is nicotine (C10H14N2), comparatively little analytical chemical work has been done on the wild species of Nicotiana. In 1934 Shmuk (lay stated that N, glauca contained an alkaloid other than nicotine that was not identified. The following year Smith (18) identified the principal alkaloid in this species as anabasine,beta-pyridyl-a'-piperi- dine. Concurrently, Shmuk and Khmura (17) reported that certain other species of Nicotiana contained alkaloids whose picrates had melting points different from that of nicotine, but again they were not identified. iV. sylvestris and crosses of this species with iV. tabacum were discussed in some detail. In 1937 Smith (19) determined the main alkaloid in Nicotiana sylvestris to be nornicotine (C9H12N2), and at approximately the same time Shmuk (16) reported: It is known that alcaloids differing in chemical structure are contained in different species of Nicotiana; thus, N. tabacum, N, rustica, N. alata, N. Langs- dor ffii all contain nicotine; N. sylvestris and N. Rusbyi [N, tomentosiformis Goodsp.] contain an alcaloid belonging to the secondary bases—^probably nornicotine, while N. glauca contains anabasine. Nicotine has been found also in Nicotiana attenuata (1), N, suave- olens (13) j and N.
    [Show full text]
  • A Model System for Tissue Culture Interventions and Genetic Engineering
    Indian Journal of Biotechnology Vol 3, April 2004, pp 171-184 Tobacco (Nicotiana tabacum L.)-A model system for tissue culture interventions and genetic engineering T R Ganapathi', P Suprasanna', P S Rao' and V A Bapat'? IPlant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India 2lndo-American Hybrid Seeds (India) Pvt Ltd, Bangalore 560 070, India Tobacco (Nicotiana tabacum L.) has become a model system for tissue culture and genetic engineering over the past several decades and continues to remain the 'Cinderella of Plant Biotechnology', An ill vitro culture medium (Murashige and Skoog, 1962), based on the studies with tobacco tissue cultures, has now been widely used as culture medium formulation for hundreds of plant species. Studies with tobacco tissue culture have shed light on the control of ill vitro growth and differentiation. Further, induction of haploids, microspore derived embryos and selection of mutant cell lines, have been achieved successfully. Tobacco has also been employed for the culture and fusion of plant protoplasts, providing invaluable information on way to explore the potential of somatic hybridization in other crops. Optimization of genetic transformation, using Agrobacterium tumefaciens and A. rhizogenes, has been central to the cascade of advances in the area of transgenic plants. Developments in the field of molecular farming for the expression and/or production of recombinant proteins, vaccines and antibodies are gaining significance for industrial use and human healthcare. Keywords: genetic transformation, molecular farming, plant biotechnology, plant cell and tissue culture, recombinant proteins, tobacco IPC Code: lnt. CI.7 A 01 H 4/00, 5/00, A 61 K 35174,35176,39/002,39/02,39/12; C 12 N 15/00, 15/01, 15/05, 15/08, 15/09 Introduction fusion and plant genetic engineering, which have Advances in plant biotechnology have made a shown tremendous potential for application in crop significant impact in the area of in vitro culture, improvement.
    [Show full text]
  • A Distinct Endogenous Pararetrovirus Family in Nicotiana Tomentosiformis, a Diploid Progenitor of Polyploid Tobacco1[W]
    A Distinct Endogenous Pararetrovirus Family in Nicotiana tomentosiformis, a Diploid Progenitor of Polyploid Tobacco1[w] Wolfgang Gregor, M. Florian Mette, Christina Staginnus, Marjori A. Matzke*, and Antonius J.M. Matzke Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, A-1090 Vienna, Austria Downloaded from https://academic.oup.com/plphys/article/134/3/1191/6112290 by guest on 28 September 2021 A distinct endogenous pararetrovirus (EPRV) family corresponding to a previously unknown virus has been identified in the genome of Nicotiana tomentosiformis, a diploid ancestor of allotetraploid tobacco (Nicotiana tabacum). The putative virus giving rise to N. tomentosiformis EPRVs (NtoEPRVs) is most similar to tobacco vein clearing virus, an episomal form of a normally silent EPRV family in Nicotiana glutinosa; it is also related to a putative virus giving rise to the NsEPRV family in Nicotiana sylvestris (the second diploid progenitor of tobacco) and in the N. sylvestris fraction of the tobacco genome. The copy number of NtoEPRVs is significantly higher in N. tomentosiformis than in tobacco. This suggests that after the polyploidiza- tion event, many copies were lost from the polyploid genome or were accumulated specifically in the diploid genome. By contrast, the copy number of NsEPRVs has remained constant in N. sylvestris and tobacco, indicating that changes have occurred preferentially in the NtoEPRV family during evolution of the three Nicotiana species. NtoEPRVs are often flanked by Gypsy retrotransposon-containing plant DNA. Although the mechanisms of NtoEPRV integration, accumulation, and/or elimination are unknown, these processes are possibly linked to retrotransposon activity. Integrated (endogenous) viral sequences are in- have originated when a pre-existing virus captured creasingly recognized as common constituents of an RT gene (Xiong and Eickbush, 1990).
    [Show full text]
  • Host Range Evolution of Potyviruses: a Global Phylogenetic Analysis
    viruses Article Host Range Evolution of Potyviruses: A Global Phylogenetic Analysis Benoît Moury * and Cécile Desbiez INRAE, Pathologie Végétale, F-84140 Montfavet, France; [email protected] * Correspondence: [email protected]; Tel.: +33-(0)4-3272-2816 Received: 12 December 2019; Accepted: 10 January 2020; Published: 16 January 2020 Abstract: Virus host range, i.e., the number and diversity of host species of viruses, is an important determinant of disease emergence and of the efficiency of disease control strategies. However, for plant viruses, little is known about the genetic or ecological factors involved in the evolution of host range. Using available genome sequences and host range data, we performed a phylogenetic analysis of host range evolution in the genus Potyvirus, a large group of plant RNA viruses that has undergone a radiative evolution circa 7000 years ago, contemporaneously with agriculture intensification in mid Holocene. Maximum likelihood inference based on a set of 59 potyviruses and 38 plant species showed frequent host range changes during potyvirus evolution, with 4.6 changes per plant species on average, including 3.1 host gains and 1.5 host loss. These changes were quite recent, 74% of them being inferred on the terminal branches of the potyvirus tree. The most striking result was the high frequency of correlated host gains occurring repeatedly in different branches of the potyvirus tree, which raises the question of the dependence of the molecular and/or ecological mechanisms involved in adaptation to different plant species. Keywords: potyvirus; potyviridae; ancestral reconstruction; discrete character; host jump; host shift; host range expansion 1.
    [Show full text]
  • Tadege, Million.Pdf
    Biographical sketch Million Tadege Million Tadege, Assistant Professor, Plant Functional Genomics Department of Plant and Soil Sciences, 368 Agricultural Hall, Stillwater, OK 74078-6028 Phone: 405-744-6193; Fax: 405-744-0354, Email: [email protected] Research Expertise Plant molecular genetics/functional genomics, control of flowering time, leaf development, genetic regulatory network in plant biomass development, retrotransposon tagging, metabolic signaling, alcoholic fermentation in plants. Education Ph.D. 1997, Plant Molecular Biology, University of Bern, Switzerland. M.Sc. 1994, Biotechnology, Wageningen Agricultural University, The Netherlands. B.Sc. 1987, Biology, Asmara University, Eritrea. Appointments 9/09 – present Assistant Professor, Oklahoma State University, OK 9/03 – 8/09 Postdoctoral Research Fellow, Samuel Roberts Noble Foundation, OK. 9/99 – 8/03 Postdoctoral Research Fellow, CSIRO, Plant Industry, Canberra, Australia. 1/98 – 8/99 Postdoctoral Research Fellow, University of Bern, IPS, Bern, Switzerland. 9/94 – 12/97 Graduate Research Assistant, University of Bern, IPS, Bern, Switzerland. 7/91 – 8/92 Lecturer, Alemaya University of Agriculture, Alemaya, Ethiopia. 8/88 – 6/91 Assistant Lecturer, Alemaya University of Agriculture, Alemaya, Ethiopia. 8/87 – 7/88 Graduate Assistant, Alemaya University of Agriculture, Alemaya, Ethiopia. Honors and Awards: 1999 - Swiss National Science Foundation Perspective Scientist Postdoctoral Award. 1997 – Excellence, Ph.D. in Plant Molecular Biology, University of Bern. 1996 - The Roche Research Foundation Student Research Award. 1992-94 - Wageningen Agricultural University Fellowship. 1987 - Great Distinction, B.Sc. in Biology, Asmara University. Professional Activities: 2010- DOE-USDA grant review panel for biomass feedstock genomics. 2005-2008, organizer of Medicago truncatula Tnt1 mutant screening public annual workshop. Reviewed papers for various scientific journals.
    [Show full text]
  • Assessing Anthocyanin Biosynthesis in Solanaceae As a Model Pathway for Secondary Metabolism
    G C A T T A C G G C A T genes Article Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism 1,2, 1,3, 1,4 1,5 Zuo Li y, Trisha L. Vickrey y, Moira G. McNally , Shirley J. Sato , Tom Elmo Clemente 1,6 and Jeffrey P. Mower 1,6,* 1 Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA 2 Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China 3 Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA 4 Biology Department, University of Jamestown, Jamestown, ND 58405, USA 5 Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA 6 Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA * Correspondence: [email protected] These authors contributed equally to this work. y Received: 19 June 2019; Accepted: 23 July 2019; Published: 25 July 2019 Abstract: Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines.
    [Show full text]