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Figure 3: Evaluation of the sensitivity of the species-specific and genus-specific LAMP tools. LAMP assays were carried out using genomic DNA extracted from P. ananatis strain CFBP3612T. Lanes 1 to 7 represent 6 ng, 600 pg, 60 pg, 6 pg, 600 fg, 60 fg of DNA and water, respectively. The detection limit of the genus-specific LAMP tool was 600 fg and 6 pg for the species-specific tool. A. Pantoea genus-specific LAMP tool. Reaction sensitivity was assessed with the naked eye.

Figure 3 Evaluation of the sensitivity of the species-specific and genus-specific LAMP tools. LAMP assays were carried out using genomic DNA extracted from P. ananatis strain CFBP3612T. Lanes 1 to 7 represent 6 ng, 600 pg, 60 pg, 6 pg, 600 fg, 60 fg of DNA and water, respectively. The detection limit of the genus-specific LAMP tool was 600 fg and 6 pg for the species-specific tool. A. Pantoea genus-specific LAMP tool. Reaction sensitivity was assessed with the naked eye.

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Continued on following page Table 1: Lists of the strains used for the taxonomic description of the genus Pantoea [40,90].
Continued on following page Table 1: Lists of the strains used for the taxonomic description of the genus Pantoea [40,90].
Figure 4: Map of the distribution of plant diseases due to infection by Pantoea ananatis (source: https://www.cabi.org/isc/datasheet/2 1909).
Figure 4: Map of the distribution of plant diseases due to infection by Pantoea ananatis (source: https://www.cabi.org/isc/datasheet/2 1909).
*Oie et al. (2008), 7Nadarasah and Stavrinides (2014), >Mergaert, Verdonck and Kersters (1993), *Brady et al. (2009a,b), *Liu et al. (2013), ©Brady et al. (2010a,b), ’Brady et a (2012), *Janisiewicz et al. (2013), *Elvira-Recuenco and van Vuurde (2000), !°McInroy and Kloepper (1995), *t Asis and Adachi (2004), **Magnani et al. (2013), ?Nadha et a (2012), **Stets et al. (2013), Brady et al. (20092,b), “Cooksey (1986), ”Guanlin (2001), “*Khetmalas et al. (1996), “Romeiro et al. (2007), “Burr et al. (1991), Brady et 4 (2011), “Gagne-Bourgue et al. (2013), “Cother et al. (2004), *Kido et al. (2008), Azad, Holmes and Cooksey (2000), “Coutinho et al, (2002), 7” Pérez-y-Terrén et al, (2009 8Fucikovsky and Aranda (2006), *Nisiotou et al. (2011), Bell et al. (2004), 3*Roper (2011), **Loiret et al. (2004), *?Verma et al. (2004), “Laskar, Nevita and Sharma (2012 3SMedrano and Bell (2007), Walcott et al. (2002), ?’Gitaitis and Gay (1997). Table 2: Epiphytic and parasitic colonisation of plants by strains of Pantoea [41,42].
*Oie et al. (2008), 7Nadarasah and Stavrinides (2014), >Mergaert, Verdonck and Kersters (1993), *Brady et al. (2009a,b), *Liu et al. (2013), ©Brady et al. (2010a,b), ’Brady et a (2012), *Janisiewicz et al. (2013), *Elvira-Recuenco and van Vuurde (2000), !°McInroy and Kloepper (1995), *t Asis and Adachi (2004), **Magnani et al. (2013), ?Nadha et a (2012), **Stets et al. (2013), Brady et al. (20092,b), “Cooksey (1986), ”Guanlin (2001), “*Khetmalas et al. (1996), “Romeiro et al. (2007), “Burr et al. (1991), Brady et 4 (2011), “Gagne-Bourgue et al. (2013), “Cother et al. (2004), *Kido et al. (2008), Azad, Holmes and Cooksey (2000), “Coutinho et al, (2002), 7” Pérez-y-Terrén et al, (2009 8Fucikovsky and Aranda (2006), *Nisiotou et al. (2011), Bell et al. (2004), 3*Roper (2011), **Loiret et al. (2004), *?Verma et al. (2004), “Laskar, Nevita and Sharma (2012 3SMedrano and Bell (2007), Walcott et al. (2002), ?’Gitaitis and Gay (1997). Table 2: Epiphytic and parasitic colonisation of plants by strains of Pantoea [41,42].
Figure 6: Alignments of the loci encoding predicted pathogenicity determinants from
Figure 6: Alignments of the loci encoding predicted pathogenicity determinants from
Figure 7: Prevalence of the mobilome and pathogenicity factors among the Pnan and Pnst strains.
Figure 7: Prevalence of the mobilome and pathogenicity factors among the Pnan and Pnst strains.
Figure 1: Typical rice leaf blight symptoms in rice fields in Bami, Mali.
Figure 1: Typical rice leaf blight symptoms in rice fields in Bami, Mali.
Figure 2: 16S rRNA standard approximation likelihood ratio tree created using Phylogeny.fr. Note that the eight isolates analysed (ASP 1, ASP 3, ASP 6, ASP 160, ASP 283, ASP 360, ASP 361 and ASP 447) do not belong to a specific species compared with sequences of 12 validated type strains of Sphingomonas species.
Figure 2: 16S rRNA standard approximation likelihood ratio tree created using Phylogeny.fr. Note that the eight isolates analysed (ASP 1, ASP 3, ASP 6, ASP 160, ASP 283, ASP 360, ASP 361 and ASP 447) do not belong to a specific species compared with sequences of 12 validated type strains of Sphingomonas species.
Figure 3: Symptoms on rice (cv. Azucena) leaves inoculated with a bacterial suspension of Sphingomonas spp., 14 days after inoculation.
Figure 3: Symptoms on rice (cv. Azucena) leaves inoculated with a bacterial suspension of Sphingomonas spp., 14 days after inoculation.
Table 2: List of PCR primers developed for the Pantoea mPCR along with the sequences of the GenBank accessions and the corresponding strains.
Table 2: List of PCR primers developed for the Pantoea mPCR along with the sequences of the GenBank accessions and the corresponding strains.
Table 4: Reaction parameters of the multiplex PCR thermocycler program.
Table 4: Reaction parameters of the multiplex PCR thermocycler program.
n.a., not applicable
n.a., not applicable
Table 1: Composition of 1 liter PGS medium Evaluation of selectivity and specificity A total of fifty pure Pantoea spp originating from Africa Rice collection were used [1,2]. They were isoleted from rice seeds and leaves collected in paddy fields in sub-Saharan Africa (Table 1 Additional file at attachement). Seven reference straines from the French Collection of Phytopatogenic Bacteria (CFBP, Angers, France), nine Xanthomonas oryzae pv. oryzae strainesand five straines of X. oryzae pv. oryzicola, nine isolates of Sphingomonas sp., nine isolates of Baccilus sp., tree isolates of Burkholderia spp., and two straines of Pseudomonas Sp were were used for the media evaluation and validation.
Table 1: Composition of 1 liter PGS medium Evaluation of selectivity and specificity A total of fifty pure Pantoea spp originating from Africa Rice collection were used [1,2]. They were isoleted from rice seeds and leaves collected in paddy fields in sub-Saharan Africa (Table 1 Additional file at attachement). Seven reference straines from the French Collection of Phytopatogenic Bacteria (CFBP, Angers, France), nine Xanthomonas oryzae pv. oryzae strainesand five straines of X. oryzae pv. oryzicola, nine isolates of Sphingomonas sp., nine isolates of Baccilus sp., tree isolates of Burkholderia spp., and two straines of Pseudomonas Sp were were used for the media evaluation and validation.
Figure 1: Photographs show that the three species P. ananatis, P. stewartii and P. agglomerans grow perfectly on all media including selective medium. However, the bacteria of the other genera (Xanthomonas, Sphingomonas, Bacillus spp. and Pseudomonas) are inhibited by the selective medium but grow perfectly on the other media (PSA and NA). A, PGS medium; B, PSA medium; C, NA medium. AA es: ee ee Lene
Figure 1: Photographs show that the three species P. ananatis, P. stewartii and P. agglomerans grow perfectly on all media including selective medium. However, the bacteria of the other genera (Xanthomonas, Sphingomonas, Bacillus spp. and Pseudomonas) are inhibited by the selective medium but grow perfectly on the other media (PSA and NA). A, PGS medium; B, PSA medium; C, NA medium. AA es: ee ee Lene
Table 1 Classification and general features of P. ananatis strains ARC297, ARC310, and ARC311
Table 1 Classification and general features of P. ananatis strains ARC297, ARC310, and ARC311
Table 3 Project information
Table 3 Project information
Table 4 Nucleotide content and gene count levels of the genomes
Table 4 Nucleotide content and gene count levels of the genomes
Strains 4, RIT273 and DAPP-PG734 belong to the species P. agglomerans and strains LMG 2632. M009 and DC283 belong to the species P. stewartii. All other strains belong to the species P. ananatis.The number of shared genes within and between species ranged from 3,400 to 3,500. Based on the ANI values, the isolates grouped with representatives of the designated species, using species cut-off values of 95% [40]. ANI values above 95% are indicated in bold face. Table 5 Average nucleotide identities (ANI) for representative strains of the species P. ananatis, P. agglomerans, and P. stewartii
Strains 4, RIT273 and DAPP-PG734 belong to the species P. agglomerans and strains LMG 2632. M009 and DC283 belong to the species P. stewartii. All other strains belong to the species P. ananatis.The number of shared genes within and between species ranged from 3,400 to 3,500. Based on the ANI values, the isolates grouped with representatives of the designated species, using species cut-off values of 95% [40]. ANI values above 95% are indicated in bold face. Table 5 Average nucleotide identities (ANI) for representative strains of the species P. ananatis, P. agglomerans, and P. stewartii
Table 1: List of P. ananatis genome sequences used for the computational evaluation of the MLVA tools.
Table 1: List of P. ananatis genome sequences used for the computational evaluation of the MLVA tools.
Table 3: Haplotype diversity of the 94 P. ananatis strains tested.
Table 3: Haplotype diversity of the 94 P. ananatis strains tested.
Figure 1: Sequence alignment of VNTR locus Loc_2 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 1: Sequence alignment of VNTR locus Loc_2 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 2: Sequence alignment of VNTR locus Loc_54 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 2: Sequence alignment of VNTR locus Loc_54 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 3: Sequence alignment of VNTR locus Loc_56 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 3: Sequence alignment of VNTR locus Loc_56 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 4: Sequence alignment of VNTR locus Loc_65 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
Figure 4: Sequence alignment of VNTR locus Loc_65 and its flanking sequences. The sequences are labeled as follows: Source of isolation Country Strain. Groups of strains are highlighted in gray for rice isolates from Africa, dark green for rice isolates from other continents and in olive green for isolates from other sources. VNTR repeats loci are highlighted in peacock blue for those isolated from the rice and in turquoise for those specific to isolates from other sources. SNPs specific to rice isolates are highlighted in gray and those specific to isolates from other sources are highlighted in olive green.
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