Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species

Frontiers in Microbiology
Małgorzata GolanowskaEwa Lojkowska

Abstract

Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expressi...Continue Reading

References

Nov 1, 1989·Molecular Microbiology·N Hugouvieux-Cotte-Pattat, J Robert-Baudouy
Jan 1, 1996·Annual Review of Microbiology·N Hugouvieux-Cotte-PattatS Reverchon
Feb 2, 1999·Molecular Plant-microbe Interactions : MPMI·T FranzaD Expert
Nov 9, 2002·Molecular Plant-microbe Interactions : MPMI·Thierry FranzaDominique Expert
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Nov 6, 2004·Microbiology·Dmitry A RodionovNicole Hugouvieux-Cotte-Pattat
Jan 11, 2011·Journal of Bacteriology·Jeremy D GlasnerNicole T Perna
May 17, 2011·BMC Genomics·Marco GalardiniEmanuele G Biondi
Jun 16, 2011·Nucleic Acids Research·You ZhouDavid S Wishart
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jun 8, 2012·Molecular Plant Pathology·John MansfieldGary D Foster
Dec 12, 2012·Environmental Microbiology·William NasserSylvie Reverchon
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Jun 4, 2013·Annual Review of Phytopathology·Alessandro M VaraniMarie-Anne Van Sluys
Jul 28, 2013·Genome Announcements·Leighton PritchardIan Toth
Nov 15, 2013·International Journal of Systematic and Evolutionary Microbiology·Jan M van der WolfShula Manulis
Feb 1, 2014·Genome Announcements·Slimane KhayiDenis Faure
Mar 15, 2014·Molecular Plant-microbe Interactions : MPMI·Marta PotrykusEwa Lojkowska
Mar 20, 2014·Bioinformatics·Torsten Seemann
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Michael IonescuSteven E Lindow
May 7, 2015·Nucleic Acids Research·Robert D FinnSean R Eddy
May 26, 2015·Nature Biotechnology·Konstantin BerlinAdam M Phillippy
Sep 5, 2015·PLoS Computational Biology·Marco GalardiniAlessio Mengoni
Nov 21, 2015·International Journal of Systematic and Evolutionary Microbiology·Imchang LeeJongsik Chun
Jun 16, 2016·Scientific Reports·Costas BouyioukosFrançois Képès

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Citations

Jul 3, 2021·International Journal of Molecular Sciences·Izabela PerkowskaAnna Ihnatowicz

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Datasets Mentioned

BETA
IFB0221
LMG25993

Methods Mentioned

BETA
PCR

Software Mentioned

EzBioCloud )
HmmerWeb
PHAST
Biopython
Prokka
MismatchCorrector
Average Nucleotide Identity Calculator (
R agricolae
Quiver
USEARCH

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