Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses

A multiplex RT-PCR method to detect papaya meleira virus complex in adult pre-flowering plants

(2020) Marlonni Maurastoni et al.   ARCHIVES OF VIROLOGY

Quantifying molecular bias in DNA data storage

(2020) Yuan-Jyue Chen et al.   Nature Communications

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

(2020) Luis Rubio et al.   Frontiers in Plant Science

Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing

(2020) Yahya Zakaria Abdou Gaafar et al.   PLoS One

G4 Structures in Control of Replication and Transcription of rRNA Genes

(2020) Kateřina Havlová et al.   Frontiers in Plant Science

Genomics Analyses of GIV and GVI Noroviruses Reveal the Distinct Clustering of Human and Animal Viruses

(2019) Lauren Ford-Siltz et al.   Viruses-Basel

High Throughput Sequencing in Plant Virus Detection and Discovery

(2019) Dan E.V. Villamor et al.   PHYTOPATHOLOGY

Global Dimensions of Plant Virus Diseases: Current Status and Future Perspectives

(2019) Roger A.C. Jones et al.   Annual Review of Virology

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

(2019) Alexander M Piper et al.   GigaScience

Quantitative real-time PCR analysis of individual flue-cured tobacco seeds and seedlings reveals seed transmission of Tobacco mosaic virus

(2019) Madeleine D. Ellis et al.   PHYTOPATHOLOGY

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

(2018) Laura E. MacConaill et al.   BMC GENOMICS

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Sweet potato feathery mottle virus and Sweet potato virus C from East Timorese and Australian Sweetpotato: Biological and Molecular Properties, and Biosecurity Implications

(2018) Solomon Maina et al.   PLANT DISEASE

Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies

(2018) Sébastien Massart et al.   PHYTOPATHOLOGY

Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids

(2018) Vicente Pallás et al.   Frontiers in Microbiology

Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

(2018) Stephen Bruinsma et al.   BMC GENOMICS

Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation

(2018) Siemon Ng et al.   Viruses-Basel

Next-Generation Sequencing Strategies

(2018) Shawn E. Levy et al.   Cold Spring Harbor Perspectives in Medicine

A multiplex reverse transcription PCR assay for simultaneous detection of six main RNA viruses in tomato plants

(2018) Huan Liu et al.   JOURNAL OF VIROLOGICAL METHODS

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Papaya ringspot virus Populations From East Timorese and Northern Australian Cucurbit Crops: Biological and Molecular Properties, and Absence of Genetic Connectivity

(2017) Solomon Maina et al.   PLANT DISEASE

Biological and Molecular Properties of a Turnip mosaic virus (TuMV) Strain that Breaks TuMV Resistances in Brassica napus

(2017) Marine G. L. Guerret et al.   PLANT DISEASE

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

(2017) Wycliff M. Kinoti et al.   Frontiers in Microbiology

Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches

(2017) Anja Pecman et al.   Frontiers in Microbiology

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing

(2017) Wycliff M. Kinoti et al.   PLoS One

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite

(2016) Kilaza Samson Mwaikono et al.   BMC MICROBIOLOGY

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

(2015) Qingfa Wu et al.   Annual Review of Phytopathology

A multiplex RT-PCR for simultaneous detection and identification of five viruses and two viroids infecting chrysanthemum

(2015) Xiting Zhao et al.   ARCHIVES OF VIROLOGY

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Plant Virus Metagenomics: Advances in Virus Discovery

(2015) Marilyn J. Roossinck et al.   PHYTOPATHOLOGY

Development of Multiplex RT-PCR for Simultaneous Detection of Garlic Viruses and the Incidence of Garlic Viral Disease in Garlic Genetic Resources

(2015) Moon Nam et al.   Plant Pathology Journal

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

The Current Incidence of Viral Disease in Korean Sweet Potatoes and Development of Multiplex RT-PCR Assays for Simultaneous Detection of Eight Sweet Potato Viruses

(2015) Hae-Ryun Kwak et al.   Plant Pathology Journal

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

(2015) Joseph Ndunguru et al.   PLoS One

Simultaneous detection of groundnut rosette assistor virus (GRAV), groundnut rosette virus (GRV) and satellite RNA (satRNA) in groundnuts using multiplex RT-PCR

(2014) S. Anitha et al.   ARCHIVES OF VIROLOGY

Simultaneous multiplex PCR detection of seven cucurbit-infecting viruses

(2014) Ji Yeon Kwon et al.   JOURNAL OF VIROLOGICAL METHODS

Development and Validation of a Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Three Papaya Viruses

(2014) Decai Tuo et al.   Viruses-Basel

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

Development of a multiplex polymerase chain reaction for simultaneous detection of wheat viruses and a phytoplasma in China

(2012) Ye Tao et al.   ARCHIVES OF VIROLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

A multiplex reverse transcription PCR assay for simultaneous detection of five tobacco viruses in tobacco plants

(2012) Jin Dai et al.   JOURNAL OF VIROLOGICAL METHODS

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

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

(2009) Jan F. Kreuze et al.   VIROLOGY

Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control

(2009) Roger A.C. Jones   VIRUS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS