Evidence for separate origins of the two <i>Pseudomonas avellanae</i> lineages

Scortichini, M.; Natalini, E.; Marchesi, U.

doi:10.1111/j.1365-3059.2006.01352.x

Cited by 12 publications

(12 citation statements)

References 35 publications

(49 reference statements)

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“…Due to low sample sizes at the field level, the partition of genetic diversity among and within fields was not considered. The results revealed that genetic diversity in Trinidad of R. solanacearum was relatively high, compared with other plant pathogenic bacteria such as Pseudomonas avellanae (Scortichini et al, 2006) or Xylella fastidiosa (Colleta-Filho & Machado, 2002). Populations were not regionally structured, as indicated by the absence of isolation by distance, suggesting that regular gene flow occurred between the regions sampled, maybe by irrigation networks, or by movement of people, equipment and plant materials among farms which can facilitate spread of strains within the island.…”

Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

“…(clonal structure), and has been reported to be widespread in bacteria (see for example Achtman, 2008or Didelot & Maiden, 2010. Rep-PCR data were previously used to infer population genetics of the hazelnut pathogen Pseudomonas avellanae (Scortichini et al, 2006), or to compare amounts and distribution of fluorescent pseudomonads genetic diversity in suppressive and conducive soils (Ramette et al, 2006). This study is the first to assess genetic structure of R. solanacearum populations at the regional scale, addressing questions related to spatial partition of genetic diversity, and genetic structure related to phylogenetic status.…”

Section: Discussionmentioning

confidence: 99%

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Wide genetic diversity of Ralstonia solanacearum strains affecting tomato in Trinidad, West Indies

et al. 2012

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The genetic diversity of Ralstonia solanacearum causing bacterial wilt of tomato in Trinidad was assessed using the hierarchical phylotyping scheme and rep-PCR DNA fingerprinting. Seventy-one isolates were collected in 2003 on infected tomato crops in the four main vegetable cropping areas of Trinidad (North, Central, South-East and South). Two phylotypes were present, with phylotype II being much more prevalent (66%) than phylotype I (34%). Phylotype II strains consisted mainly of sequevar 7 in Central and South-East, and sequevar 35 in North, South-East and South. This is the first report of sequevar 7 outside southeastern USA. In contrast, no 'brown rot' (phylotype IIB ⁄ 1, race 3 biovar 2) or emerging strains of phylotype IIB ⁄ 4NPB were identified. Rep-PCR data were used to assess population genetic structure. No significant clustering by geographical distance was found, suggesting regular gene flow among cropping areas (via waterways, plant or soil). However, the population from Central was significantly differentiated from the others, containing only phylotype II ⁄ seq 7 strains, with a high degree of clonality, suggesting a possible recent introduction from abroad. The South population was less aggressive and more genetically diverse, suggesting horizontal gene transfers within the population, even among isolates of different phylotypes. Phylotype I and phylotype II populations differed slightly in clonality levels, with indications of more frequent recombination events within phylotype I populations. Possible factors influencing genetic diversity and distribution within the island are discussed.

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Wide genetic diversity of Ralstonia solanacearum strains affecting tomato in Trinidad, West Indies

et al. 2012

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“…This hypothesis cannot be ruled out also because in many areas of walnut cultivation in Southern Europe, Minor Asia and Central Asia the production is still largely based on the cultivation of J. regia ecotypes, which are well adapted to a typical environment [36], and Xaj could adapt accordingly. A geographic structure for phytopathogenic bacteria has been demonstrated for Pseudomonas avellanae [37,38] and Ralstonia solanacearum [12].…”

Section: Discussionmentioning

confidence: 98%

Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

Marcelletti¹,

Ferrante²,

Scortichini³

2010

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Forty-five Xanthomonas arboricola pv. juglandis (Xaj) strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST), using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity

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“…avellanae populations found in Greece and Italy, and these differences were considered to be representative of the variability of the species. Therefore, two different lineages belonging to the same species were recognized and retained as originating separately [10] but evolving similarly to infect cultivated hazelnut trees [11]. …”

Section: Introductionmentioning

confidence: 99%

A Genomic Redefinition of Pseudomonas avellanae species

et al. 2013

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The circumscription of bacterial species is a complex task. So far, DNA-DNA hybridization (DDH), 16S rRNA gene sequencing, and multiocus sequence typing analysis (MLSA) are currently the preferred techniques for their genetic determination. However, the average nucleotide identity (ANI) analysis of conserved and shared genes between two bacterial strains based on the pair-wise genome comparisons, with support of the tetranucleotide frequency correlation coefficients (TETRA) value, has recently been proposed as a reliable substitute for DDH. The species demarcation boundary has been set to a value of 95-96% of the ANI identity, with further confirmation through the assessment of the corresponding TETRA value. In this study, we performed a genome-wide MLSA of 14 phytopathogenic pseudomonads genomes, and assessed the ANI and TETRA values of 27 genomes, representing seven out of the nine genomospecies of Pseudomonas spp. sensu Gardan et alii, and their phylogenetic relationships using maximum likelihood and Bayesian approaches. The results demonstrate the existence of a well demarcated genomic cluster that includes strains classified as P. avellanae, P. syringae pv. theae, P. s. pv. actinidiae and one P. s. pv. morsprunorum strain all belonging to the single species P. avellanae. In addition, when compared with P. avellanae, five strains of P. s. pv. tomato, including the model strain DC3000, and one P. s. pv. lachrymans strain, appear as very closely related to P. avellanae, with ANI values of nearly 96% as confirmed by the TETRA analysis. Conversely, one representative strain, previously classified as P. avellanae and isolated in central Italy, is a genuine member of the P. syringae species complex and can be defined as P. s. pv. avellanae. Currently. The core and pan genomes of P. avellanae species consist of 3,995 and 5,410 putative protein-coding genes, respectively.

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Evidence for separate origins of the two Pseudomonas avellanae lineages

Cited by 12 publications

References 35 publications

Wide genetic diversity of Ralstonia solanacearum strains affecting tomato in Trinidad, West Indies

Wide genetic diversity of Ralstonia solanacearum strains affecting tomato in Trinidad, West Indies

Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

A Genomic Redefinition of Pseudomonas avellanae species

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