Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

Frontiers in Microbiology
Mélanie MassonnetDario Cantu

Abstract

The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor ...Continue Reading

References

Jan 18, 1976·Biochimica Et Biophysica Acta·M K Wassef, J W Hendrix
Jul 1, 1987·Molecular Biology and Evolution·N Saitou, M Nei
Dec 17, 2002·The Journal of General and Applied Microbiology·Makoto KimuraIsamu Yamaguchi
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Jul 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Koichiro TamuraSudhir Kumar
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Jun 14, 2005·Nature Genetics·Simon Wong, Kenneth H Wolfe
Sep 14, 2006·Molecular Microbiology·Jin Woo BokNancy P Keller
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Dec 13, 2007·Nucleic Acids Research·Joshua D PodlevskyJulian J-L Chen
Nov 1, 2008·Current Opinion in Microbiology·Ellen M Fox, Barbara J Howlett
Dec 2, 2008·Nucleic Acids Research·Genis ParraIan Korf
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Apr 14, 2009·Methods in Enzymology·Kira J Weissman
Apr 14, 2009·Methods in Enzymology·Russell J Cox, Thomas J Simpson
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jun 19, 2009·Chemical Reviews·Stefan BräseCarl F Nising
Jun 27, 2009·PLoS Pathogens·Jeffrey J Coleman, Eleftherios Mylonakis
Sep 15, 2009·Comptes rendus biologies·Philippe LarignonChristophe Bertsch
Dec 3, 2009·Human Genomics·David R Nelson
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Aug 20, 2010·Fungal Genetics and Biology : FG & B·Yuntao DaiYanli Wang
Sep 21, 2010·Applied and Environmental Microbiology·Jeroen G NijlandArnold J M Driessen
Nov 26, 2010·Nature Methods·Can AlkanEvan E Eichler
Mar 29, 2011·Molecular Phylogenetics and Evolution·Kristiina NygrenHanna Johannesson
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Feb 2, 2012·Toxins·Anna AndolfiAntonio Evidente
Feb 16, 2012·Molecular Biology and Evolution·Eve W L ChowJames A Fraser
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 13, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Gabriela AguiletaLilian Gout
Mar 23, 2012·PloS One·Candice N HanseyC Robin Buell
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
May 9, 2012·Nature Reviews. Microbiology·Sylvain Raffaele, Sophien Kamoun
May 31, 2012·Nucleic Acids Research·Yanbin YinYing Xu

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Datasets Mentioned

BETA
SRP126240
PRJNA421316

Methods Mentioned

BETA
Illumina sequencing
PCR
RNAseq

Software Mentioned

fPoxDB
DESeq2
GATK
EvidentialGene
MUMmer
FastaAlternateReferenceMaker
dbCAN
FigTree
NUCmer
SPAdes

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