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

Frontiers in Microbiology
Anja PecmanMaja Ravnikar

Abstract

Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for vi...Continue Reading

References

Jan 5, 2002·Molecular Plant-microbe Interactions : MPMI·A ItayaB Ding
Jan 3, 2009·Virus Research·Sead SabanadzovicIoannis E Tzanetakis
Aug 1, 2009·Journal of Virological Methods·Ion Gutiérrez-AguirreMaja Ravnikar
May 10, 2013·Phytopathology·Maher Al RwahnihMysore R Sudarshana
Dec 24, 2013·Virus Research·Neil BoonhamRick Mumford
Jul 9, 2014·Annual Review of Microbiology·Ricardo FloresSantiago F Elena
Jun 10, 2015·Phytopathology·Marilyn J RoossinckPhilippe Roumagnac
Nov 5, 2015·Nature Reviews. Molecular Cell Biology·Filipe Borges, Robert A Martienssen
Nov 28, 2015·The Plant Journal : for Cell and Molecular Biology·Konstantin I IvanovKristiina Mäkinen
Jun 3, 2016·Virology Journal·Marike VisserHans J Maree

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Citations

Apr 17, 2018·Electrophoresis·Tamara MartinovićDjuro Josić
Jan 11, 2019·PLoS Pathogens·Michael Goodin, Antonia Dos Reis Figueira
Feb 26, 2019·Phytopathology·D E V VillamorI E Tzanetakis
Sep 14, 2018·Frontiers in Plant Science·Hans J MareeThierry Candresse
Sep 7, 2018·Scientific Reports·Yeonhwa JoWon Kyong Cho
Aug 24, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Konstantina KatsarouKriton Kalantidis
Aug 9, 2020·Frontiers in Plant Science·Luis RubioInmaculada Ferriol
Jun 6, 2018·Frontiers in Microbiology·Johanna Santala, Jari P T Valkonen
Oct 15, 2018·BMC Genomics·Yeonhwa Jo, Won Kyong Cho
Aug 1, 2020·Plants·György PasztorEva Varallyay
Jun 12, 2019·Archives of Virology·S J WylieH Li
Oct 13, 2020·Frontiers in Microbiology·Nicolás BejermanRalf G Dietzgen
Dec 8, 2020·Frontiers in Microbiology·Yahya Z A GaafarHeiko Ziebell
Nov 17, 2020·Plant Disease·Gustavo A Díaz-Cruz, Bryan J Cassone
Jul 27, 2018·Current Opinion in Virology·Shahideh NouriBryce W Falk
Mar 12, 2021·Frontiers in Microbiology·Amy H FitzpatrickPaul Cotter
Dec 1, 2018·Current Opinion in Virology·Anna E WhitfieldRalf G Dietzgen
Apr 4, 2021·Viruses·Gajanan T MehetreBhim Pratap Singh
Apr 4, 2021·Viruses·Solomon MainaBrendan C Rodoni
Jun 8, 2021·Frontiers in Microbiology·Mark Paul Selda RivarezDenis Kutnjak
Aug 13, 2021·Frontiers in Microbiology·Elisa Navas-HermosillaJesús Navas-Castillo
Aug 10, 2021·Frontiers in Plant Science·Leonardo Velasco, Carlos V Padilla

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Datasets Mentioned

BETA
KY810782
JX866666.1

Methods Mentioned

BETA
electron microscopy
ELISA
reverse transcription quantitative PCR
Illumina sequencing

Software Mentioned

BLASTx
CLC Genomics Workbench
CLC Genomic Workbench

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