Genome-Enhanced Detection and Identification (GEDI) of plant pathogens

PeerJ
Nicolas FeauRichard C Hamelin

Abstract

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% o...Continue Reading

References

Mar 13, 1999·Medical Mycology·J LöfflerH Einsele
Nov 5, 1999·Methods in Molecular Biology·S Rozen, H Skaletsky
Jul 5, 2002·Clinical Microbiology Reviews·Siew Fah Yeo, Brian Wong
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Jun 24, 2004·Mycological Research·Kelly L IvorsMatteo Garbelotto
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Feb 16, 2010·BMC Evolutionary Biology·Haining LinC Robin Buell
Aug 13, 2010·Nature·Clive Brasier, Joan Webber
May 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sébastien DuplessisFrancis Martin
May 1, 2009·Molecular Ecology Resources·Keith A Seifert
May 1, 2009·Molecular Ecology Resources·Agathe VialleRichard C Hamelin
Mar 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Conrad L SchochUNKNOWN Fungal Barcoding Consortium Author List
Apr 14, 2012·Nature·Matthew C FisherSarah J Gurr
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Sep 6, 2013·Annual Review of Genomics and Human Genetics·Cadhla Firth, W Ian Lipkin
Dec 4, 2013·Nucleic Acids Research·Igor V GrigorievIgor Shabalov
Mar 8, 2014·Fungal Genetics and Biology : FG & B·Frank N MartinMichael D Coffey
Mar 19, 2014·Trends in Plant Science·Luigi Faino, Bart P H J Thomma
Mar 25, 2014·Computers in Biology and Medicine·Sándor M Szilágyi, László Szilágyi
Apr 29, 2014·Malaria Journal·Edwin KamauChristian F Ockenhouse
Jun 5, 2014·BMC Microbiology·Tomasz GosiewskiMałgorzata Bulanda
Sep 30, 2014·Computational Biology and Chemistry·Juan Esteban GalloOliver Keatinge Clay
Dec 17, 2014·Microbial Ecology·Marco PautassoOttmar Holdenrieder
Dec 19, 2014·BMC Genomics·Mostafa M AbbasPonnuraman Balakrishnan
Mar 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Braham DhillonRichard C Hamelin
Sep 24, 2015·Veterinary Record Open·C HänselF Melzer

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Citations

Jan 2, 2020·Evolutionary Applications·Richard C Hamelin, Amanda D Roe
Dec 17, 2020·PLoS Neglected Tropical Diseases·Wilson LimWendy Wj van de Sande

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Methods Mentioned

BETA
PCR
electrophoresis
PCR-ELISA

Software Mentioned

MUSCLE
AUGUSTUS
OrthoMCL
ABySS
BLASTp
BLASTn
PRIMER3
trans

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