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dc.contributor.authorIdris, Ali
dc.contributor.authorAl-Saleh, Mohammed
dc.contributor.authorPiatek, Marek J.
dc.contributor.authorAl-Shahwan, Ibrahim
dc.contributor.authorAli, Shahjahan
dc.contributor.authorBrown, Judith K.
dc.date.accessioned2014-08-27T09:49:19Z
dc.date.available2014-08-27T09:49:19Z
dc.date.issued2014-03-12
dc.identifier.citationIdris A, Al-Saleh M, Piatek M, Al-Shahwan I, Ali S, et al. (2014) Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput Sequencing. Viruses 6: 1219-1236. doi:10.3390/v6031219.
dc.identifier.issn19994915
dc.identifier.pmid24625811
dc.identifier.doi10.3390/v6031219
dc.identifier.urihttp://hdl.handle.net/10754/325365
dc.description.abstractTraditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes) (genus, Begomovirus; family, Geminiviridae) were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA). Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS). CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions. 2014 by the authors; licensee MDPI, Basel, Switzerland.
dc.language.isoen
dc.publisherMDPI AG
dc.rightsThis article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
dc.subjectGeminivirus
dc.subjectGenome enrichment
dc.subjectIllumina sequencing
dc.subjectssDNA viruses
dc.subjectViral genome assembly
dc.subjectDNA helicase
dc.subjectsatellite DNA
dc.subjectsingle stranded DNA
dc.subjectBegomovirus
dc.subjectcontrolled study
dc.subjectDNA sequence
dc.subjectgene mapping
dc.subjectgenetic code
dc.subjectgenome analysis
dc.subjecthigh throughput sequencing
dc.subjectmetagenomics
dc.subjectNicotiana benthamiana
dc.subjectnucleotide sequence
dc.subjectparsimony analysis
dc.subjectphylogeny
dc.subjectplant virus
dc.subjectpolymerase chain reaction
dc.subjectrestriction fragment length polymorphism
dc.subjectsingle nucleotide polymorphism
dc.subjecttomato yellow leaf curl betasatellite
dc.subjectTomato yellow leaf curl virus
dc.subjectvirus genome
dc.titleViral metagenomics: Analysis of begomoviruses by illumina high-throughput sequencing
dc.typeArticle
dc.contributor.departmentBioscience Core Lab
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentDesert Agriculture Initiative
dc.identifier.journalViruses
dc.identifier.pmcidPMC3970147
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Plant Protection, King Saud University, Riyadh 11451, Saudi Arabia
dc.contributor.institutionSchool of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personIdris, Ali
kaust.personAli, Shahjahan
kaust.personPiatek, Marek J.
refterms.dateFOA2018-06-13T15:19:47Z


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