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VIROIDS and SATELLITES Cover photographs Front cover Electron micrograph of small circular coconut cadang-cadang viroid molecules. (Courtesy John W. Randles.) Coconut cadang-cadang viroid induced non-necrotic yellow spotting of a coconut palm leaflet (right) compared with an asymptomatic leaflet (left). (Courtesy John W.Randles.) Potato spindle tuber viroid affected potato tuber showing typical spindle shape (right) compared with a normal potato tuber (left). (Courtesy Theodor O.Diener.) Extreme leaf chlorosis (peach calico) symptoms induced by certain variants of peach latent mosaic viroid. (Courtesy Francesco Di Serio and Ricardo Flores.) Symptoms of citrus exocortis viroid infection on a citron fruit (right) compared with anormal fruit (left).(Courtesy Joseph S.Semancik.) Severe symptoms of a variant of cucumber mosaic virus Tfn-satellite RNA on tomato fruit cv. Italpeel. (Courtesy Donato Gallitelli and the late Makis Vovlas.) Symptoms of the dapple apple variant of apple scar skin viroid on apple fruit cv.Starkrimson. (Courtesy Jean-ClaudeDesvignes.) Back cover Symptoms of chrysanthemum stunt viroid on white chrysanthemum flower (right) showing reduced size and quality compared with a normalflower (left). (Courtesy Teruo Sano.) Avocado sunblotch viroid induced depression and distortion symptoms on anavocado fruit. (Courtesy David N.Kuhn.) VIROIDS and SATELLITES Edited by A H HMED ADIDI U.S.DepartmentofAgriculture,Beltsville,MD,UnitedStates R F ICARDO LORES PolytechnicUniversityofValencia-CSIC,Valencia,Spain J W. R OHN ANDLES TheUniversityofAdelaide,WaiteCampus,GlenOsmond,Australia P P ETER ALUKAITIS SeoulWomen’sUniversity,Seoul,SouthKorea AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1800,SanDiego,CA92101-4495,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyrightr2017ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronic ormechanical,includingphotocopying,recording,oranyinformationstorageandretrievalsystem, withoutpermissioninwritingfromthepublisher.Detailsonhowtoseekpermission,further informationaboutthePublisher’spermissionspoliciesandourarrangementswithorganizationssuch astheCopyrightClearanceCenterandtheCopyrightLicensingAgency,canbefoundatourwebsite: www.elsevier.com/permissions. Thisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythe Publisher(otherthanasmaybenotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperience broadenourunderstanding,changesinresearchmethods,professionalpractices,ormedicaltreatment maybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluating andusinganyinformation,methods,compounds,orexperimentsdescribedherein.Inusingsuch informationormethodstheyshouldbemindfuloftheirownsafetyandthesafetyofothers,including partiesforwhomtheyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assume anyliabilityforanyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability, negligenceorotherwise,orfromanyuseoroperationofanymethods,products,instructions,orideas containedinthematerialherein. BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-12-801498-1 ForInformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:SaraTenney AcquisitionEditor:LindaVersteeg-Buschman EditorialProjectManager:FentonCoulthurst ProductionProjectManager:ChrisWortley CoverDesigner:MilesHitchen TypesetbyMPSLimited,Chennai,India List of Contributors Mazen Alazem Institute of Plant and Microbial Biology, Academia Sinica, Taipei,Taiwan HaniZ.Al-Tuwariqi MinistryofAgriculture,Riyadh,SaudiArabia Marina Barba CREA-Research Centre for Plant Protection and Certification, Rome,Italy Iraklis N. Boubourakas Directorate of Rural Economy and Veterinary of Piraeus,AtticaPrefecture,Attica,Greece KadriyeÇag˘layan MustafaKemalUniversity,Antakya,Turkey ThierryCandresse INRAandUniversityofBordeaux,Bordeaux,France VicenteConejero PolytechnicUniversityofValencia-CSIC,Valencia,Spain Elena Dadami RLP AgroScience, AlPlanta-Institute for Plant Research, Neustadt-Mußbach,Germany Athanasios Dalakouras RLP AgroScience, AlPlanta-Institute for Plant Research,Neustadt-Mußbach,Germany Jose´-AntonioDaro`s PolytechnicUniversityofValencia-CSIC,Valencia,Spain MarcosDelaPenã PolytechnicUniversityofValencia-CSIC,Valencia,Spain SoniaDelgado PolytechnicUniversityofValencia-CSIC,Valencia,Spain FrancescoDiSerio NationalResearchCouncil,Bari,Italy JonathanDixon SeekaKiwifruitIndustriesLimited,TePuke,NewZealand Nuria Duran-Vila Valencian Institute of Agricutural Research-IVIA, Valencia, Spain KhaledA.El-Dougdoug AinShamsUniversity,Cairo,Egypt AmineElleuch UniversityofSfax,Sfax,Tunisia Francesco Faggioli CREA-Research Centre for Plant Protection and Certification,Rome,Italy RicardoFlores PolytechnicUniversityofValencia-CSIC,Valencia,Spain Aurora Fraile Center for Plant Biotechnology and Genomics, Polytechnic UniversityofMadrid-INIA,Madrid,Spain SelmaGago-Zachert LeibnizInstituteofPlantBiochemistry,Halle,Germany DonatoGallitelli UniversityofBariAldoMoro,Bari,Italy Fernando Garcıá-Arenal Center for Plant Biotechnology and Genomics, PolytechnicUniversityofMadrid-INIA,Madrid,Spain xxv xxvi LISTOFCONTRIBUTORS Andrew D.W. Geering The University of Queensland, St Lucia, QLD, Australia LucianoGiunchedi UniversityofBologna,Bologna,Italy GustavoGo´mez PolytechnicUniversityofValencia-CSIC,Valencia,Spain EbenezerA.Gyamera UniversityofCambridge,Cambridge,UnitedKingdom Nuredin Habili The University of Adelaide, Waite Campus, Glen Osmond, SA,Australia AhmedHadidi U.S.DepartmentofAgriculture,Beltsville,MD,UnitedStates Vipin Hallan CSIR-Institute ofHimalayan BioresourceTechnology, Palampur, HimachalPradesh,India Rosemarie W. Hammond U.S. Department of Agriculture, Beltsville, MD, UnitedStates Dagmar Hanold The University of Adelaide, Waite Campus, Glen Osmond, SA,Australia TatsujiHataya HokkaidoUniversity,Sapporo,Japan CarmenHernańdez PolytechnicUniversityofValencia-CSIC,Valencia,Spain NiHong HuazhongAgriculturalUniversity,Wuhan,China MunetakaHosakawa KyotoUniversity,Kyoto,Japan Yau-HeiuHsu NationalChungHsingUniversity,Taichung,Taiwan Chung-ChiHu NationalChungHsingUniversity,Taichung,Taiwan Ying-WenHuang NationalChungHsingUniversity,Taichung,Taiwan Delano James Centre for Plant Health-Canadian Food Inspection Agency, NorthSaanich,BC,Canada HendryJoseph UniversitiTeknologiMARA(Sabah),Sabah,Malaysia KritonKalantidis UniversityofCrete,Heraklion,Greece MariaS.Kaponi Formerly,HirosakiUniversity,Hirosaki,Japan Mikyeong Kim National Institute of Agricultural Sciences, RDA, Wanju-gun, SouthKorea GaryR.Kinard U.S.DepartmentofAgriculture,Beltsville,MD,UnitedStates LihL.Kong UniversitiPutraMalaysia,Selangor,Malaysia Natalia Kovalskaya U.S. Department of Agriculture, Beltsville, MD, United States DavidN.Kuhn U.S.DepartmentofAgriculture,Miami,FL,UnitedStates PanayotaE.Kyriakopoulou AgriculturalUniversityofAthens,Athens,Greece IreneLavagi UniversityofCalifornia,Riverside,CA,UnitedStates Shi-FangLi ChineseAcademyofAgriculturalSciences,Beijing,China Na-Sheng Lin Institute of Plant and Microbial Biology, Academia Sinica, Taipei,Taiwan Kai-ShuLing U.S.DepartmentofAgriculture,Charleston,SC,UnitedStates Ming-RuLiou NationalChungHsingUniversity,Taichung,Taiwan xxvii LISTOFCONTRIBUTORS PurificaciońLisoń PolytechnicUniversityofValencia-CSIC,Valencia,Spain Amparo Lo´pez-Carrasco Polytechnic University of Valencia-CSIC, Valencia, Spain Marta Luigi CREA-Research Centre for Plant Protection and Certification, Rome,Italy Ańgel-Emilio Martıńez de Alba Polytechnic University of Valencia-CSIC, Valencia,Spain TizianaMascia UniversityofBariAldoMoro,Bari,Italy ChikaraMasuta HokkaidoUniversity,Sapporo,Japan JaroslavMatousˇek AcademyofSciencesoftheCzechRepublic(ASCR), Cˇeske´ Budeˇjovice,CzechRepublic Marie-ChristineMaurel SorbonneUniversity,Paris,France EllisT.M.Meekes Naktuinbouw,Roelofarendsveen,TheNetherlands SofiaMinoia PolytechnicUniversityofValencia-CSIC,Valencia,Spain BeatrizNavarro NationalResearchCouncil,Bari,Italy XianzhouNie AgricultureandAgri-FoodCanada,Fredericton,NB,Canada Robert A. Owens U.S. Department of Agriculture, Beltsville, MD, United States VicentePalla´s PolytechnicUniversityofValencia-CSIC,Valencia,Spain PeterPalukaitis SeoulWomen’sUniversity,Seoul,SouthKorea Dattaraj B. Parakh ICAR-National Bureau of Plant Genetic Resources, New Delhi,India Jean-PierrePerreault UniversityofSherbrooke,Sherbrooke,QC,Canada Edward V. Podleckis U.S. Department of Agriculture, Riverdale, MD, United States JesseD.Pyle HarvardMedicalSchool,Boston,MA,UnitedStates John W. Randles The University of Adelaide, Waite Campus, Glen Osmond, SA,Australia DetlevRiesner HeinrichHeineUniversity,Du¨sseldorf,Germany M.JudithB.Rodriguez PhilippineCoconutAuthority,Albay,Philippines Johanna W. Roenhorst National Plant Protection Organization, Wageningen, TheNetherlands Marilyn J. Roossinck Pennsylvania State University, University Park, PA, UnitedStates LuisaRubino NationalResearchCouncil,Bari,Italy Jesus A. Sańchez-Navarro Polytechnic University of Valencia-CSIC, Valencia, Spain TeruoSano HirosakiUniversity,Hirosaki,Japan Karen-Beth G. Scholthof Texas A&M University, College Station, TX, United States xxviii LISTOFCONTRIBUTORS PedroSerra PolytechnicUniversityofValencia-CSIC,Valencia,Spain HanakoShimura HokkaidoUniversity,Sapporo,Japan RudraP.Singh AgricultureandAgri-FoodCanada,Fredericton,NB,Canada DijanaSˇkoric´ UniversityofZagreb, Zagreb,Croatia GiuseppeStancanelli EuropeanFoodSafetyAuthority,Parma,Italy GerhardSteger HeinrichHeineUniversityDu¨sseldorf,Germany Anna Taglienti CREA-Research Centre for Plant Protection and Certification, Rome,Italy MatildeTessitori UniversityofCatania,Catania,Italy SathisS.Thanarajoo UniversitiPutraMalaysia,Selangor,Malaysia Antonio Tiberini Mediterranea University of Reggio Calabria, Reggio Calabria,Italy EnzaM.Torchetti NationalResearchCouncil,Bari,Italy MinaTsagris UniversityofCrete,Crete,Greece TaroTsushima HirosakiUniversity,Hirosaki,Japan GanesanVadamalai UniversitiPutraMalaysia,Selangor,Malaysia Jacobus Th.J. Verhoeven National Plant Protection Organization, Wageningen,TheNetherlands GeorgiosVidalakis UniversityofCalifornia,Riverside,CA,UnitedStates Qiao-ChunWang NorthwestA&FUniversity,Xianyang,China Michael Wassenegger RLP AgroScience, AlPlanta-Institute for Plant Research, Neustadt-Mußbach,Germany Stephan Winter Leibniz Institute, DSMZ- German Collection of MicroorganismsandCellCultures,Braunschweig,Germany Wen-XingXu HuazhongAgriculturalUniversity,Wuhan,China XiulingYang ChineseAcademyofAgriculturalSciences,Beijing,China Yongjiang Zhang Chinese Academy of Inspection and Quarantine, Beijing, China ZhiboZhang NorthwestA&FUniversity,Xianyang,China Xueping Zhou Chinese Academy of Agricultural Sciences, Beijing, China; ZhejiangUniversity,Hangzhou,China ShuifangZhu ChineseAcademyofInspectionandQuarantine,Beijing,China Foreword I am delighted to write a Foreword for this well-conceived book, which, with the prominent authors chosen, is assured to take its place as an up-to-date, complete, and dependable textbook on the plant- infecting subviral viroids and satellites for years to come. The third majorextensioninthe history ofthe biospherewas ushered in by the discovery of viroids in 1971, following the earlier discoveries of the “subvisible” microorganisms by Antonie van Leeuwenhoek in 1675 and of the “submicroscopic” viruses by Dmitri Iosifovich Ivanovsky in 1892. The status of viroids is recognized by the International Committee for Virus Taxonomy (ICTV) with the creation of a new order of subviral agents, which currently includes two families, eightgenera, and32 species of viroids. A great interest in viroids among plant virologists occurred immedi- ately after their discovery and the important biological, biochemical, and evolutionary significance of subviral agents has been acknowledged by many other scientists who confirmed the fundamental nature of viroids (and, implicitly, of other subviral agents), which, like viruses, are replicated in infected cells. It is now accepted that viroids, like viruses, share the most character- istic property of living beings: in an appropriate environment, they are able to generate copies of themselves; in other words, they are endowed with autonomous replication (and evolution). It is in this framework that viroids represent the frontier of life (infectious agents consisting of only 246(cid:1)401 ribonucleotides), an aspect that should attract the atten- tion of anybody interested in biology. TheodorO. Diener xxix Preface Many plant diseases currently known to be caused by viroids were first recognized because of their damaging economic impact many years ago.PotatospindletuberdiseasewasfirstdescribedintheUnitedStates in the early 1920s and its infectious agent was identified by Theodor O. Diener of the US Department of Agriculture, Beltsville, Maryland, in 1971. He described it as a free RNA of 25,000(cid:1)110,000 Daltons, much smallerthanaviralgenome,andnameditas“viroid”in1972.Similarly, the “exocortis” disease of citrus was first described in the late 1940s in the United States and in 1972, Joseph S. Semancik of the University of California, Riverside, showed that its causal agent is also a viroid of 125,000 Daltons. Cadang-cadang disease of coconut palms in the Philippines, so named because it leads to the premature decline and deathoftrees,wasfirstdescribedearlyinthe20thcenturybutitwasnot until 1975 that John W. Randles of the University of Adelaide, South Australia,demonstratedthatthediseaseiscausedbyaviroid.By1977,it was found that viroids cause economically important diseases in vegetable crops, fruit trees, ornamentals, and palm species. The host range of viroids has expanded over the years to include grapevine and other cultivated and wild plant species. Viroid molecules are very small circular RNAs, ranging from 246 to 401 nucleotides in length and with a high degree of internal base-pairing. Their discovery has challenged the central dogma of genetic inheritance because unlike viruses they are naked and lack protein-coding ability. Although found only in plants, their discovery paved the way for other subviral agents such as prions and hepatitis delta virus to be recognized as pathogens of eukaryotic organisms.ViroidsarethesmallestknowninfectiousRNAs. Basil Kassanis of the Rothamsted Experiment Station, Harpenden, Hertfordshire, UK, coined the name “satellite” in 1962 for very small virus particles he found in some cultures of tobacco necrosis virus (TNV). He demonstrated that these 17-nm viral satellite particles were unable to replicate in the absence of the larger 30-nm TNV particles. Similarly, in 1972 Irving R. Schneider of the US Department of Agriculture in Beltsville found nonessential but biologically active satellite RNA molecules in preparations of various other viruses. In 1972, a devastating disease epidemic swept through tomato fields of the French Alsace province destroying the crop. The causal agent was not revealed until 1977, when Jacobus M. Kaper of the US Department of Agriculture xxxi