Top

Published in:

Open Access 01-12-2018 | Short Report

Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing

Authors: Reina Teresa Martínez, Mariana Martins Severo de Almeida, Rosalba Rodriguez, Athos Silva de Oliveira, Fernando Lucas Melo, Renato Oliveira Resende

Published in: Virology Journal | Issue 1/2018

Abstract

The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.

Simoes AJG, Hidalgo CA. The economic complexity observatory: an analytical tool for understanding the dynamics of economic development. Workshops at The Twenty-Fifth AAAI Conference on Artificial Intelligence. 2011;2011:29–42.

Plyusnin A, Beaty BJ, Elliot RM, Goldbach R, Kormelink R, Lundkvist Å, Schmaljohn CS, Tesh RB. Family Bunyaviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Virus taxonomy: ninth report of the international committee on taxonomy of viruses. San Diego: Elsevier; 2012. p. 725–41.

Martínez RT, Poojari S, Tolin SA, Cayetano X, Naidu RA. First report of Tomato spotted wilt virus in peppers and tomato in the Dominican Republic. Plant Dis. 2013; https://doi.org/10.1094/PDIS-06-13-0617-PDN.

Almeida MMS, Orílio AF, Melo FL, Rodriguez R, Feliz A, Cayetano X, Martínez RT, Resende RO. The first report of Tomato chlorotic spot virus (TCSV) infecting long beans and chili peppers in the Dominican Republic. Plant Dis. 2014;https://doi.org/10.1094/PDIS-04-14-0348-PDN.

Batuman O, Rojas MR, Almanzar A, Gilbertson RL. First report of Tomato chlorotic spot virus in processing tomatoes in the Dominican Republic. Plant Dis. 2013; https://doi.org/10.1094/PDIS-07-13-0685-PDN.

Pappu HR, Jones RAC, Jain RK. Global status of tospovirus epidemics in diverse cropping systems: successes achieved and challenges ahead. Virus Res. 2009;141:219–36.CrossRefPubMed

Sela N, Luria N, Dombrovsky A. Genome assembly of bell pepper endornavirus from small RNA. J Virol. 2012; https://doi.org/10.1128/JVI.00983-12.

Jo Y, Choi H, Cho WK. De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data. Genome Announc. 2015; https://doi.org/10.1128/genomeA.00061-15.

Alcala-Briseno RI, Coskan S, Londoño MA, Polston JE. Genome sequence of Southern tomato virus in asymptomatic tomato ‘sweet hearts’. Genome Announc. 2017; https://doi.org/10.1128/genomeA.01374-16.

10.

Jo Y, Choi H, Yoon JY, Choi SK, Cho WK. In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses. Gene. 2016;575:712–7.CrossRefPubMed

11.

Roossinck MJ. Plant virus ecology. PLoS Pathog. 2013; https://doi.org/10.1371/journal.ppat.1003304.

12.

Xu P, Chen F, Mannas JP, Feldman T, Sumner LW, Roossinck MJ. Virus infection improves drought tolerance. New Phytol. 2008;180:911–21.CrossRefPubMed

13.

Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.CrossRefPubMedPubMedCentral

14.

Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704.CrossRefPubMed

15.

Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27:221–4.CrossRefPubMed

16.

Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012; https://doi.org/10.1038/nmeth.2109.

17.

Londoño A, Capobianco H, Zhang S, Polston JE. First record of Tomato chlorotic spot virus in the USA. Tropi Plant Pathol. 2012;37:333–8.CrossRef

18.

Warfield CY, Clemens K, Adkins S. First report of Tomato chlorotic spot virus on annual vinca (Catharanthus roseus) in the United States. Plant Dis. 2015; https://doi.org/10.1094/PDIS-12-14-1269-PDN.

19.

Webster CG, Reitz SR, Perry KL, Adkins S. A natural M RNA reassortant arising from two species of plant- and insect-infecting bunyaviruses and comparison of its sequence and biological properties to parental species. Virol. 2011;413:216–25.CrossRef

20.

Fukuhara T, Gibbs MJ. Family Endornaviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Virus taxonomy: ninth report of the international committee on taxonomy of viruses. San Diego: Elsevier; 2012. p. 519–21.

21.

Okada R, Kiyota E, Sabanadzovic S, Moriyama H, Fukuhara T, Saha P, Rossinck MJ, Severin A, Valverde RA. Bell pepper endornavirus: molecular and biological properties, and occurrence in the genus capsicum. J. Gen. Virol. 2011;92:2664–73.CrossRefPubMed

22.

Kwon SJ, Tan SH, Vidalakis G. Complete nucleotide sequence and genome organization of an endornavirus from bottle gourd (Lagenaria siceraria) in California. USA Virus Genes. 2014;49:163–8.CrossRefPubMed

23.

Chen B, Bernards M, Wang A. Complete genome sequence of a bell pepper endornavirus isolate from Canada. Genome Announc. 2015; https://doi.org/10.1128/genomeA.00905-15.

24.

Boccardo G, Lisa V, Luisoni E, Milne RG. Cryptic plant viruses. Adv Virus Res. 1987;32:171–214.CrossRefPubMed

25.

Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE. Southern tomato virus: the link between the families Totiviridae and Partitiviridae. Virus Res. 2009;140:130–7.CrossRefPubMed

26.

Padmanabhan C, Zheng Y, Li R, Sun SE, Zhang D, Liu Y, Fei Z, Ling KS. Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh. Genome Announc. 2015; https://doi.org/10.1128/genomeA.01226-15.

27.

Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res. 2014;188:128–41.CrossRefPubMed

28.

Valverde RA, Gutierrez DL. Transmission of a dsRNA in bell pepper and evidence that it consists of the genome of an endornavirus. Virus Genes. 2007;35:399–403.CrossRefPubMed

29.

Valverde RA, Gutierrez DL. Molecular and biological properties of a putative partitivirus from jalapeño pepper (Capsicum annuum L.). Rev Mexic fitopatol. 2008;26:1–6.

30.

Sabanadzovic S, Valverde RA. Properties and detection of two cryptoviruses from pepper (Capsicum annum). Virus Genes. 2011;43:307–12.CrossRefPubMed

31.

Valverde RA, Nameth ST, Jordan RL. Indigenous double-stranded RNA from pepper (Capsicum annuum). Plant Sci. 1990;74:255–8.

32.

Saritha RK, Jain P, Baranwal VK, Jain RK, Srivastava A, Kalia P. First report of Pepper cryptic virus 2 in chilli (Capsicum annuum) in India. Virus Dis. 2016;27:327–8.CrossRef

33.

Sun M, Jing CC, Wu GT, Sun XC, Liu Y, Qing L. First report of Pepper cryptic virus 2 infecting pepper in China. J Plant Pathol. 2017; http://sipav.org/main/jpp/index.php/jpp/article/view/3808.

34.

Candresse T, Marais A, Faure C. First report of Southern tomato virus on tomatoes in Southwest France. Plant Dis. 2013; https://doi.org/10.1094/PDIS-01-13-0017-PDN.

35.

Verbeek M, Dullemans AM, Espino A, Botella M, Alfaro-Fernández A, Font MI. First report of southern tomato virus in tomato in the Canary Islands, Spain. J Plant Pathol. 2015; http://sipav.org/main/jpp/index.php/jpp/article/view/3356.

36.

Lockhart BE, Menke J, Dahal G, Olszewski NE. Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome. J Gen, Virol. 2000;81:1579–85.CrossRef

37.

Horiuchi H, Fukuhara T. Putative replication intermediates in Endornavirus, a novel genus of plant dsRNA viruses. Virus Genes. 2004;29:365–75.CrossRefPubMed

38.

Staginnus C, Gregor W, Mette MF, Teo CH, Borroto-Fernández EG, Machado MLC, Matzke M, Schwarzacher T. Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol. 2007; https://doi.org/10.1186/1471-2229-7-24.

39.

Ávila AC, Huguenot C, Resende RO, Kitajima EW, Goldbach RW, Peters D. Serological differentiation of 20 isolates of tomato spotted wilt virus. J. Gen. Virol. 1990;71:2801–7.CrossRefPubMed

40.

Ávila AC, Haan P, Kormelink R, Resende RO, Goldbach RW, Peters D. Classification of tospoviruses based on phylogeny of nucleoprotein gene sequences. J Gen Virol. 1993;74:153–9.CrossRefPubMed

41.

Dewey RA, Semorile LC, Grau O, Crisci JV. Cladistic analysis of Tospovirus using molecular characters. Mol Phylogenet Evol. 1997;8:11–32.CrossRefPubMed

42.

Nagata T, Ávila AC, Tavares PCTM, Barbosa CJ, Juliatti FC, Kitajima EW. Occurrence of different tospoviruses in six states of Brazil. Fitopatol Bras. 1990;20:90–4.

43.

Ávila AC, Lima MF, Resende RO, Pozzer L, Ferraz E, Maranhão EAA, Candeia JA, Costa ND. Identificação de tospovírus em hortaliças no Submédio São Francisco utilizando DAS-ELISA e DOT-ELISA. Fitopatol Bras. 1996;21:503–8.

44.

Lima MF, Ávila AC, Resende RO, Nagata T. Levantamento e identificação de espécies de Tospovirus em tomateiro e pimentão no Submédio do Vale São Francisco e no Distrito Federal. Summa Phytopathol. 2000;26:205–10.

45.

Eiras M, Costa IFD, Chaves ALR, Colariccio A, Harakava R, Tanaka FAO, Garcêz RM, Silva LA. First report of a tospovirus in a commercial crop of cape gooseberry in Brazil. New Dis Rep. 2012; https://doi.org/10.5197/j.2044-0588.2012.025.025.

46.

Webster CG, Perry KL, Lu X, Hosman L, Frantz G, Mellinger C, Adkins S. First report of Groundnut ringspot virus infecting tomato in South Florida. Plant Health Prog. 2010; https://doi.org/10.1094/PHP-2010-0707-01-BR.

47.

Webster CG, Jensen CE, Rivera-Vargas LI, Rodrigues JCV, Frantz G, Mellinger HC, Adkins S. First report of Tomato chlorotic spot virus (TCSV) in tomato, pepper, and jimsonweed in Puerto Rico. Plant Health Prog. 2013; https://doi.org/10.1094/PHP-2013-0812-01-BR.

48.

Webster CG, Frantz G, Reitz SR, Funderburk JE, Mellinger HC, McAvoy E, Turechek WW, Marshall SH, Tantiwanich Y, McGrath MT, Daughtrey ML, Adkins S. Emergence of Groundnut ringspot virus and Tomato chlorotic spot virus in vegetables in Florida and the southeastern United States. Phytopathology. 2015;105:388–98.CrossRefPubMed

49.

Adegbola RO, Fulmer AM, Williams B, Brenneman TB, Kemerait RC, Sheard W, Woodward JE, Adkins S, Naidu RA. First report of the natural occurrence of Tomato chlorotic spot virus in peanuts in Haiti. Plant Dis. 2016; https://doi.org/10.1094/PDIS-01-16-0070-PDN.

50.

USDA, Plant protection and quarantine: helping U.S. agriculture thrive—across the country and around the world. In: annual report. United States Department of Agriculture. 2016. https://www.aphis.usda.gov/publications/plant_health/report-ppq-2016.pdf. Accessed 20 July 2017.

51.

Pimentel D. Plant pathogens and quarantines and the implication for global trade and world food. In: Loebenstein G, Thottappilly G, editors. Virus and virus-like diseases of major crops in developing countries. Dordrecht: Kluwer Academic; 2003. p. 79–89.CrossRef

52.

Patoka J, Bláha M, Kalous L, Vrabec V, Buřič M, Kouba A. Potential pest transfer mediated by international ornamental plant trade. Sci Rep. 2016;6:25896.CrossRefPubMedPubMedCentral

Title: Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing
Authors: Reina Teresa Martínez
Mariana Martins Severo de Almeida
Rosalba Rodriguez
Athos Silva de Oliveira
Fernando Lucas Melo
Renato Oliveira Resende
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: Virology Journal / Issue 1/2018
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-018-0931-9

ACC 2024 Congress Coverage

Heart Failure Video

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing

Abstract

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 1/2018

Transcriptome profiling of whitefly guts in response to Tomato yellow leaf curl virus infection

Hepatitis B infection and preeclampsia among pregnant Sudanese women

Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes

Trigger factor assisted self-assembly of canine parvovirus VP2 protein into virus-like particles in Escherichia coli with high immunogenicity

Clinical validation of REALQUALITY RQ-HPV Screen according to the international guidelines for human papillomavirus DNA test requirements for cervical screening

Rescue and characterization of recombinant cedar virus, a non-pathogenic Henipavirus species

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page