Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani

BMC Genomics

Research Article

Kok-Gan Chan¹  Teik-Min Chong¹  Valérie Hélias²  Frédérique Van Gijsegem³  Denis Faure⁴  Pauline Blin⁴  Slimane Khayi⁵  Jacques Pédron⁶  Mohieddine Moumni⁷ 

[1] Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia;Fédération Nationale des Producteurs de Plants de Pomme de Terre-Recherche développement Promotion du Plant de Pomme de Terre (FN3PT-RD3PT), 75008, Paris, France;UMR 1349 IGEPP INRA - Agrocampus Ouest Rennes, 35653, LeRheu, France;INRA, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint Bernard, 75005, Paris, France;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;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;Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco;UPMC Univ Paris 06, UMR 7618, IEES Paris (Institute of Ecology and Environmental Sciences), 7 Quai Saint bernard, 75005, Paris, France;Université Moulay Ismaïl, Faculté des Sciences, Département de Biologie, Meknès, Morocco;

关键词: Dickeya;    Soft rot;    Potato;    Population genomics;    Horizontal gene transfer;   

DOI  :  10.1186/s12864-015-1997-z

 received in 2015-06-19, accepted in 2015-10-03,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundDickeya 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.ResultsWe 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 IPO2222T) 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.ConclusionsThis 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.

【 授权许可】

CC BY   
© Khayi et al. 2015