title: Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani.
abstract: BACKGROUND
  Dickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.
  
  
  RESULTS
  We combined Illumina and PacBio technologies to complete the genome sequence of D. solani strain 3337 that was used as a reference to compare with 19 other genomes (including that of the type strain IPO2222(T)) which were generated by Illumina technology. This population genomic analysis highlighted an unexpected variability among D. solani isolates since it led to the characterization of two distinct sub-groups within the D. solani species. This approach also revealed different types of variations such as scattered SNP/InDel variations as well as replacing and additive horizontal gene transfers (HGT). Infra-species (between the two D. solani sub-groups) and inter-species (between D. solani and D. dianthicola) replacing HGTs were observed. Finally, this work pointed that genetic and functional variation in the motility trait could contribute to aggressiveness variability in D. solani.
  
  
  CONCLUSIONS
  This work revealed that D. solani genomic variability may be caused by SNPs/InDels as well as replacing and additive HGT events, including plasmid acquisition; hence the D. solani genomes are more dynamic than that were previously proposed. This work alerts on precautions in molecular diagnosis of this emerging pathogen.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France. slimane.khayi@i2bc.paris-saclay.fr.|Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco. slimane.khayi@i2bc.paris-saclay.fr.
authors.forename: Slimane
authors.initials: S
authors.lastname: Khayi
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France. Pauline.Blin@i2bc.paris-saclay.fr.
authors.forename: Pauline
authors.initials: P
authors.lastname: Blin
authors.affiliation: UPMC Univ Paris 06, UMR 7618, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint bernard, 75005, Paris, France. jacques.pedron@upmc.fr.
authors.forename: Jacques
authors.initials: J
authors.lastname: Pédron
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. cluster1986@hotmail.com.
authors.forename: Teik-Min
authors.initials: TM
authors.lastname: Chong
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. kokgan@um.edu.my.
authors.forename: Kok-Gan
authors.initials: KG
authors.lastname: Chan
authors.affiliation: Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco. mmoumni02@yahoo.fr.
authors.forename: Mohieddine
authors.initials: M
authors.lastname: Moumni
authors.affiliation: Fédération Nationale des Producteurs de Plants de Pomme de Terre-Recherche développement Promotion du Plant de Pomme de Terre (FN3PT-RD3PT), 75008, Paris, France. valerie.helias@fnpppt.fr.|UMR 1349 IGEPP INRA - Agrocampus Ouest Rennes, 35653, LeRheu, France. valerie.helias@fnpppt.fr.
authors.forename: Valérie
authors.initials: V
authors.lastname: Hélias
authors.affiliation: INRA, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint Bernard, 75005, Paris, France. frederique.van_gijsegem@agroparistech.fr.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Van Gijsegem
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Avenue de la Terrasse, 91198, Gif-sur-Yvette cedex, France. denis.faure@i2bc.paris-saclay.fr.
authors.forename: Denis
authors.initials: D
authors.lastname: Faure
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D004755:Enterobacteriaceae / Q000235:genetics* / Q000472:pathogenicity; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005828:Genetics, Population; D016680:Genome, Bacterial; D056186:Metagenomics; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D011198:Solanum tuberosum / Q000382:microbiology