Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput SequencingReportar como inadecuado

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Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia


Department of Plant Protection, King Saud University, Riyadh 11451, Saudi Arabia


School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA

Update on Address Information 12 August 2015: School of Plant Sciences, University of Arizona Tucson, AZ 85741, USA; Email:, Phone: +1-520-665-1041


Author to whom correspondence should be addressed.

Abstract Traditional 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. View Full-Text

Keywords: Illumina sequencing; geminivirus; ssDNA viruses; genome enrichment; viral genome assembly Illumina sequencing; geminivirus; ssDNA viruses; genome enrichment; viral genome assembly

Autor: Ali Idris 1,†,* , Mohammed Al-Saleh 2, Marek J. Piatek 1, Ibrahim Al-Shahwan 2, Shahjahan Ali 1 and Judith K. Brown 3



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