46 and Kodon v2 software (Applied Maths NV, Sint-Martens-Latem,

4.6 and Kodon v.2 software (Applied Maths NV, Sint-Martens-Latem, Belgium). The genome sequences of the following eight strains were compared, to assess the variability of gyrB: S. maltophilia strain k279a, AM743169; S. maltophilia strain R551-3, NC_011071; Stenotrophomonas sp. strain SKA 14, NZ_ACDV00000000; X. campestris, pv campestris, strain ATCC 33913T, NC_003902; X. campestris pv. vesicatoria, strain 85-10, NC_007508; X. albilineans strain GPE PC73, NC_013722; X. axonopodis pv. citri, strain 306, NC_003919; and X. oryzae pv. oryzae, strain KACC 10331, NC_006834. The levels of nucleotide variation, in segments of 50 nucleotides,

along the entire gene were see more calculated. Similarly, the sequences of the two gyrB regions selleck chemical for the 12 type strains of the Stenotrophomonas spp. were compared. Genomic DNA–DNA reassociation analysis was carried out, using the hybridization protocols described previously (Urdiain et al., 2008). Labelled reference DNA from S. maltophilia type strain CCUG 5866T was hybridized to the unlabelled target DNA. Hybridization mixtures contained 150 ng of labelled DNA and 15 μg of target DNA in a total volume of 72 μL. The mixtures were incubated

for 16 h at 72 °C. Each strain hybridization was performed in duplicate, and the mean values and standard deviations were calculated. Stenotrophomonas are associated with various ecosystems and clinical conditions (Berg et al., 1999) and is one of the most commonly isolated species from nosocomial infections (Morrison et al., 1986; Senol, 2004; Wakino et al., 2009) and respiratory samples of patients with CF (Ballestero et al., 1995; Denton, 1997; Goss et al., 2004; Marzuillo et al., 2009). The species within the genus Stenotrophomonas exhibit only limited phenotypic characteristics, and the 16S rRNA gene sequence similarity is high. The original

aim of this study was to assess the applicability of gyrB analyses for reliable species delineation in Stenotrophomonas, using the primers designed for Pseudomonas (Yamamoto et al., 2000), that is gyrB Region 1. While this study was underway, an analysis of Xanthomonas spp., using a different region of the gyrB, was published (Young et al., 2008; Parkinson et al., 2009). Given the close phylogenetic proximity of Xanthomonas to Stenotrophomonas (Moore et al., 1997), Interleukin-2 receptor this region, that is gyrB Region 2 in this study, also was used for comparative sequence analysis of the Stenotrophomonas spp. The sequences have been deposited in GenBank; the accession numbers are listed in Table 1. Figure 1 presents a comparison of the numbers of variable positions within the two different regions. The publicly available complete sequences of the gyrB genes of three strains of Stenotrophomonas spp. and five strains of Xanthomonas spp. were compared, and the number of variable nucleotide positions within gyrB was determined.

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