CORE Metadata, citation and similar papers at core.ac.uk Provided by Diposit Digital de la Universitat de Barcelona Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era Journal: Molecular Plant Pathology Manuscript ID: MPP-PP-13-026.R1 Manuscript Type: Pathogen Profile Date Submitted by the Author: n/a Complete List of Authors: Peeters, Nemo; INRA UMR441 Laboratoire des Interactions Plantes Micro- organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 cheminProof de borde rouge, Auzeville CS52627 Guidot, Alice; INRA UMR441 Laboratoire des Interactions Plantes Micro- organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627 Vailleau, Fabienne; INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; Université de Toulouse ; INP ; ENSAT, 18 chemin de Borde Rouge Valls, Marc; Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CRAG)., Edifici CRAG, Campus UAB Keywords: Ralstonia solanacearum Page 1 of 26 1 2 3 4 1 5 6 7 1 Ralstonia solanacearum , a widespread bacterial plant pathogen in the post-genomic era 8 2 Nemo Peeters 1,2* , Alice Guidot 1,2 , Fabienne Vailleau 1,2, 3 and Marc Valls 4 9 10 3 *corresponding author, [email protected] , +33 561285592 11 12 4 1-INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM) 24 chemin de Borde 13 5 Rouge – Auzeville CS 52627 31326 CASTANET TOLOSAN CEDEX, FRANCE 14 15 6 2-CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM) 24 chemin de Borde 16 7 Rouge – Auzeville CS 52627 31326 CASTANET TOLOSAN CEDEX, France 17 18 8 3-Université de Toulouse ; INP ; ENSAT ; 18 chemin de Borde Rouge, 31326 Castanet Tolosan, France. 19 9 4-Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics 20 10 (CRAG). Edifici CRAG, Campus UAB, 08193 BELLATERRA, CATALONIA, SPAIN 21 22 11 23 24 12 25 26 27 Proof 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 2 of 26 1 2 3 4 2 5 6 7 1 Ralstonia solanac earum 8 2 Taxonomy: Bacteria; Proteobacteria; β subdivision; Ralstonia group; genus Ralstonia 9 10 3 Microbiological properties: Gram-negative, aerobic, motile rod 11 12 4 Disease sym ptoms: Agent of bacterial wilt of solanaceaous plants characterized by a sudden wilt of 13 5 the whole plant. Typically, stem cross-sections ooze a slimy bacterial exudate. R. solanacearum is Formatted: Font: Italic 14 6 also the agent of Moko disease of banana and brown rot of potato. Formatted: Font: Not Italic 15 16 7 Disease control: Pathogen-free seed and transplants. Existence of a few resistant and tolerant plant 17 8 varieties. Prophylactic sanitation practices and cultural rotations. 18 19 9 20 10 Since the last Ralstonia solanacearum pathogen profile was published ten years ago (Genin & 21 22 11 Boucher, 2002), the studies concerning this plant pathogen have definitely taken the genomic and 23 12 post-genomic avenue. This was pioneered by the first sequenced and annotated genome for a major 24 13 plant bacterial pathogen (Salanoubat et al.et al. , 2002) and followed by many more genomes in the 25 14 years after. All molecular features studied have now a genomic flavor ., In the future, this will help to 26 15 connect the classical field pathology and diversity studies with gene content of specific strains . This 27 16 contributes to a global understanding of R. solanacearumProof virulence mechanisms . Figure 1 highlights 28 17 some features specific to R. solanacearum and also displays different plant bioassays. 29 30 18 31 32 19 33 20 A classification in four phylotypes Formatted: Normal, Line spacing: single 34 35 21 In pace with the development of molecular tools, classification of R. solanacearum has undergone Formatted: Space After: 10 pt, Line spacing: 36 22 many changes during the past 10 years. In 2005, Fegan and Prior proposed a new hierarchical Multiple 1.15 li 37 23 classification based upon the analysis of the sequence of the ITS (Internal Transcribed Spacer) region, 38 24 the hrpB and the endoglucanase ( egl ) genes. The analysis of 140 R. solanacearum strains isolated 39 25 from all over the world revealed a subdivision of the species into four phylotypes, which are 40 41 26 correlated with the strains’ geographical origins. Phylotype I includes strains originating primarily 42 27 from Asia, Phylotype II those from America, Phylotype III those from Africa, and Phylotype IV those 43 28 from Indonesia, Australia and Japan. This phylotype IV also contains the two close relatives of R. 44 29 solanacearum : Ralstonia syzygii and the blood disease bacterium (BDB) strains. A multiplex PCR 45 30 based upon sequence information from the ITS region has been developed to rapidly identify the 46 31 phylotype to which a strain belongs (Fegan & Prior, 2005). Each phylotype can be further subdivided 47 32 in groups of strains named sequevars, or sequence variants, according to the egl nucleotidic 48 33 sequence. More than 50 sequevars have been defined so far. 49 50 34 This classification was confirmed by comparative genomic hybridization of a set of 18 strains, Formatted: Line spacing: Multiple 1.15 li 51 35 representing the biodiversity of R. solanacearum on a microarray representative of the GMI1000 52 36 reference strain genome (Guidot et al.et al. , 2007). Genomic data for nine new R. solanacearum 53 37 strains also confirmed this classification (Remenant et al. , 2010, Remenant et al. , 2011, Remenant et Field Code Changed 54 38 al. , 2012). Thanks to the overwhelming phylogenetic data on phylotype II strains -, it has been 55 56 57 58 59 60 Page 3 of 26 1 2 3 4 3 5 6 7 1 suggested that this phylotype should be divided in two subgroups IIA and IIB (Castillo & Greenberg, 8 2 2007, Cellier et al. , 2012). One can’t exclude that deeper sampling in the other phylotypes may 9 3 alsonot result in a similar refinement of classification. 10 4 The geographic isolation, and not host preference, has been the main driver of the separation of R. Formatted: Space After: 10 pt, Line spacing: 11 Multiple 1.15 li 12 5 solanacearum strains into four phylotypes (Castillo & Greenberg, 2007, Wicker et al. , 2012). Using 13 6 coalescent genealogy reconstruction, Wicker et al. (2012) suggested that R. solanacearum originated 14 7 from the Australian/Indonesian region where phylotype IV strains are found. A subgroup of the 15 8 ancestral strains from this region From the Australian/Indonesian region, a subgroup of the ancestral 16 9 strains probably spread throughout the present Austral-Eastern Africa and Madagascar, and 17 10 differentiated later in phylotype III and phylotype I (predicted with an East African/Asian origin). 18 11 Another subgroup of ancestral strains migrated to the actual Brazil and differentiated later into the 19 12 subgroups IIA and IIB at a time similar to that of the phylotype I/III differentiation, possibly before 20 13 the fragmentation of Gondwana (Castillo & Greenberg, 2007, Wicker et al. et al. , 2012) . 21 22 14 23 24 15 25 16 A species complex, let’s keep it simple Formatted: Normal, Line spacing: single 26 27 Proof 17 A species complex is defined as a cluster of closely-related isolates whose individual members may Formatted: Space After: 10 pt, Line spacing: 28 18 represent more than one species. The term ‘species complex’ was first applied to R. solanacearum by Multiple 1.15 li 29 19 Gillings et al. (1993) to reflect the phenotypic and genotypic variability within the species. Taghavi et 30 31 20 al. (1996) then confirmed the concept of the R. solanacearum species complex by including R. syzygii 32 21 and BDB strains into the R. solanacearum phylogeny. Studies of DNA-DNA similarity revealed that the 33 22 relatedness between R. solanacearum isolates is often just under the 70% threshold level commonly 34 23 expected within a species (Roberts et al. , 1990). By comparing different strains to the phylotype I Field Code Changed 35 24 strain GMI1000 by microarray hybridization, the most divergent strains still have 68-69% of their 36 25 genes hybridizing with the GMI1000 oligonucleotides (Guidot et al. et al. , 2007). More recently, 37 26 Remenant et al. (2010; 2011) used Average Nucleotide Identity (ANI) to evaluate genetic distances 38 27 between the eight sequenced genomes from this species complexcalculate genomic distances 39 28 between all sequenced genomes in the species complex . From the results , based on the ANI>95% 40 29 cut-off (Konstantinidis & Tiedje, 2005, Konstantinidis et al. , 2006) the authors suggested that the R. 41 30 solanacearum species complex should be restructured into three different species: one containing 42 31 phylotype I and III, a second containing phylotype II, and a third containing phylotype IV including R. 43 32 syzygii and BDB strains (Remenant et al. et al. , 2011). The ANI provides a more robust and accurate Formatted: English (U.S.) 44 45 33 measurement of the genetic distance than the DNA-DNA hybridization (Konstantinidis & Tiedje, 46 34 2005). However, as pointed out by Konstantinidis and Tiedje (200 56), the ANI should not be 47 35 considered as the sole argument for species definition (Konstantinidis & Tiedje, 2005). Ecological 48 36 niche occupation which is a justifiable measurement of the phenotypic potential of a bacterial strain, 49 37 is another important argument for species definition (Konstantinidis et al.