Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2015 Oct 7

PMID 26439260

Citations 44

Authors

Joseph Ndunguru

Peter Sseruwagi

Fred Tairo

Francesca Stomeo

Solomon Maina

Appolinaire Djikeng

Appolinaire Djinkeng

Monica Kehoe

Laura M Boykin

Affiliations

Soon will be listed here.

Abstract

Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.

Citing Articles

prediction of candidate gene targets for the management of African cassava whitefly (, SSA1-SG1), a key vector of viruses causing cassava brown streak disease.

Kaweesi T, Colvin J, Campbell L, Visendi P, Maslen G, Alicai T PeerJ. 2024; 12:e16949.

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Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda.

Nyirakanani C, Tamisier L, Bizimana J, Rollin J, Nduwumuremyi A, Bigirimana V Virus Evol. 2023; 9(2):vead053.

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References

Padidam M, Sawyer S, Fauquet C . Possible emergence of new geminiviruses by frequent recombination. Virology. 1999; 265(2):218-25. DOI: 10.1006/viro.1999.0056. View

Martin D, Rybicki E . RDP: detection of recombination amongst aligned sequences. Bioinformatics. 2000; 16(6):562-3. DOI: 10.1093/bioinformatics/16.6.562. View

Gibbs M, Armstrong J, GIBBS A . Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics. 2000; 16(7):573-82. DOI: 10.1093/bioinformatics/16.7.573. View

Posada D, Crandall K . Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A. 2001; 98(24):13757-62. PMC: 61114. DOI: 10.1073/pnas.241370698. View

Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z . Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol. 2002; 83(Pt 6):1511-1521. DOI: 10.1099/0022-1317-83-6-1511. View

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

Susko E, Inagaki Y, Roger A . On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol Biol Evol. 2004; 21(9):1629-42. DOI: 10.1093/molbev/msh159. View

Smith J . Analyzing the mosaic structure of genes. J Mol Evol. 1992; 34(2):126-9. DOI: 10.1007/BF00182389. View

Martin D, Posada D, Crandall K, Williamson C . A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses. 2005; 21(1):98-102. DOI: 10.1089/aid.2005.21.98. View

10.

Fauquet C, Fargette D . International Committee on Taxonomy of Viruses and the 3,142 unassigned species. Virol J. 2005; 2:64. PMC: 1208960. DOI: 10.1186/1743-422X-2-64. View

11.

Chare E, Holmes E . A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol. 2005; 151(5):933-46. DOI: 10.1007/s00705-005-0675-x. View

12.

Gascuel O, Steel M . Neighbor-joining revealed. Mol Biol Evol. 2006; 23(11):1997-2000. DOI: 10.1093/molbev/msl072. View

13.

Rosenberg N . Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution. 2007; 61(2):317-23. DOI: 10.1111/j.1558-5646.2007.00023.x. View

14.

Boni M, Posada D, Feldman M . An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics. 2007; 176(2):1035-47. PMC: 1894573. DOI: 10.1534/genetics.106.068874. View

15.

Ross H, Murugan S, Li W . Testing the reliability of genetic methods of species identification via simulation. Syst Biol. 2008; 57(2):216-30. DOI: 10.1080/10635150802032990. View

16.

Rodrigo A, Bertels F, Heled J, Noder R, Shearman H, Tsai P . The perils of plenty: what are we going to do with all these genes?. Philos Trans R Soc Lond B Biol Sci. 2008; 363(1512):3893-902. PMC: 2607417. DOI: 10.1098/rstb.2008.0173. View

17.

Mbanzibwa D, Tian Y, Tugume A, Mukasa S, Tairo F, Kyamanywa S . Genetically distinct strains of Cassava brown streak virus in the Lake Victoria basin and the Indian Ocean coastal area of East Africa. Arch Virol. 2009; 154(2):353-9. DOI: 10.1007/s00705-008-0301-9. View

18.

Kreuze J, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I . Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology. 2009; 388(1):1-7. DOI: 10.1016/j.virol.2009.03.024. View

19.

Adams I, Glover R, Monger W, Mumford R, Jackeviciene E, Navalinskiene M . Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol. 2009; 10(4):537-45. PMC: 6640393. DOI: 10.1111/j.1364-3703.2009.00545.x. View

20.

Winter S, Koerbler M, Stein B, Pietruszka A, Paape M, Butgereitt A . Analysis of cassava brown streak viruses reveals the presence of distinct virus species causing cassava brown streak disease in East Africa. J Gen Virol. 2010; 91(Pt 5):1365-72. DOI: 10.1099/vir.0.014688-0. View