MultiLocus Sequence Analysis- and Amplified Fragment Length Polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species

Hamza, Abdou Azali; Robène-Soustrade, Isabelle; Jouen, Emmanuel; Lefeuvre, Pierre; Chiroleu, Frédéric; Saux, M. Fisher-Le; Gagnevin, Lionel; Pruvost, Olivier

doi:10.1016/j.syapm.2011.12.005

Cited by 42 publications

(42 citation statements)

References 39 publications

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“…Isolates of X. euvesicatoria from Australian capsicum and chilli crops were genetically similar to isolates from overseas based on phylogenetic analysis of the atpD, efp, dnaK, and gyrB genes (Ah-You et al 2009;Hamza et al 2010Hamza et al , 2012. Australian isolates of X. euvesicatoria were positive in the X. euvesicatoria species-specific PCR, supporting the grouping of these isolates in the MLSA phylogeny.…”

Section: Discussionsupporting

confidence: 51%

“…Isolates of X. vesicatoria from tomato identified in this study separated into two strongly supported subclades that each contained at least one isolate identified as X. vesicatoria by Hamza et al (2012). The X. vesicatoria-specific PCR detected the Australian isolates from both subclades.…”

Section: Discussionmentioning

confidence: 60%

“…AtpD sequence was included in this MLSA as its absence did not significantly alter the tree topology and its inclusion better differentiated X. euvesicatoria and X. perforans clades. The recombination events detected in atpD by Hamza et al (2012) were not detected by RDP in the single gene or concatenated data sets of these isolates. The species delimitation results supported the relatedness seen in the above phylogenies (supplementary Table 5).…”

Section: Mlsamentioning

confidence: 82%

“…PCRs were performed as described in Koenraadt et al (2009) using 2.5 U of MangoTaq™ (Bioline) and 1 μl of template. Primers and their annealing temperatures are listed in Table 2. MLSA-PCR primers targeting the chaperone protein dnaK (dnaK), elongation factor P (efp), ATP synthase subunit beta (atpD) and DNA gyrase subunit B (gyrB) genes (Table 2) were used as described (Boudon et al 2005;Ah-You et al 2009;Ngoc et al 2010;Hamza et al 2012). Annealing temperatures were optimised for the MLSA primers targeting all four genes.…”

Section: Biochemical Analysis and Pathogenicitymentioning

confidence: 99%

“…atpD, dnaK, efp, and gyrB genes (supplementary Table 3) available on GenBank (Benson et al 2005) using clustalW (Larkin et al 2007). Sequences from Hamza et al (2010Hamza et al ( , 2012 and the top BLASTn hit for each gene of isolates in unresolved clades were included in the MLSA analysis. The outgroup taxa were Stenotrophomonas maltophilia, X. albilineans and X. campestris pv.…”

Section: Biochemical Analysis and Pathogenicitymentioning

confidence: 99%

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Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

Roach

Mann

Gambley³

et al. 2017

Eur J Plant Pathol

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Several species of Xanthomonas cause bacterial leaf spot, a disease that affects solanaceous crops worldwide. The diversity of 64 Australian isolates of Xanthomonas spp. associated with bacterial leaf spot in tomato, capsicum and chilli crops in eastern Australia was determined using multi-locus sequence analysis of atpD, dnaK, efp and gyrB genes, species-specific PCR assays and biochemical analyses. At least five species of Xanthomonas associated with bacterial leaf spot were identified in Australian tomato, capsicum and chilli crops and their pathogenicity assessed. Phylogenetic and biochemical analyses identified X. euvesicatoria, X. perforans and X. vesicatoria as the most frequently recovered pathogenic species. Non-pathogenic and weakly pathogenic species were also identified. The suitability of the identification methods used and the implications of the detection of these species will be discussed.Keywords amylolytic . pectolytic . Solanaceae . disease management IntroductionBacterial leaf spot (BLS) is a disease of solanaceous crops that occurs worldwide, especially in warm and humid climates (Jones et al. 2014). Several species of Xanthomonas are reported to cause BLS of tomato (Solanum lycopersicum), capsicum and chilli (Capsicum annuum) . The symptoms of BLS are small, brown, angular, water-soaked lesions on leaves, stems and fruit, and result in defoliation and direct fruit damage. Severe infection may result in extensive damage to crops with significant yield losses (Pernezny et al. 2003). Species reported to cause BLS all produce similar symptoms on their hosts, making precise diagnosis difficult from visual symptoms alone. The impact of pathological convergence and importance of phylogenetic testing in the case of BLS are further highlighted by Hajri et al. (2009). The causal bacteria are spread by wind and water, and may survive in crop residues, weeds and volunteer plants (Jones et al. 1986). A link between field disease and seed contamination has Eur J Plant Pathol (2018) 150:595-608

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Section: Discussionsupporting

confidence: 51%

Section: Discussionmentioning

confidence: 60%

Section: Mlsamentioning

confidence: 82%

Section: Biochemical Analysis and Pathogenicitymentioning

confidence: 99%

Section: Biochemical Analysis and Pathogenicitymentioning

confidence: 99%

See 3 more Smart Citations

Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

Roach

Mann

Gambley³

et al. 2017

Eur J Plant Pathol

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Prevalence of HPV and variation of HPV 16/HPV 18 E6/E7 genes in cervical cancer in women in South West China

Yang

et al. 2014

Journal of Medical Virology

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Genetic variations of High-Risk HPV E6/E7 may be associated with the development of cervical cancer in specific geographic regions. Few data have been reported about the HPV prevalence and E6/E7 variants among cervical cancer patients in Southwest China. This study was designed to investigate the prevalence of HPV and E6/E7 variants of most prevalent HPV among cervical cancer patients in Southwest China. After genotyping, E6/E7 genes of most prevalent HR HPV samples were sequenced and analyzed. Phylogenetic trees were then constructed, followed by an analysis of the diversity of secondary structure and selection pressures. HPV 16 (73.8%) and HPV 18 (16.4%) are the most prevalent infection types among cervical cancer patients, followed by HPV 58, HPV 56 and HPV 59, which is different from the high HPV 58 infection rate of outpatients in this region. Eighteen single nucleotide changes were observed in HPV 16 E6 with 13/18 non-synonymous mutations (5 in beta sheet and 2 in alpha helix). Ten single nucleotide changes were identified among HPV 16 E7 with 3/10 non-synonymous mutations. Three single nucleotide changes were observed in HPV 18 E6 with one non-synonymous mutation, and only one synonymous mutation was identified in HPV 18 E7. HPV 16 E6-D25E, E7-N29S and E7-T846C (S95S) exhibited a prevalent linkage mutation. The phylogenetic tree demonstrates that European and Asian lineages were the main patterns. This study may help understand the intrinsic geographical relatedness and oncogenic potential of HR HPV and contributes further to research of diagnostic, therapeutic and therapeutic vaccine strategy.

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AFLP protocol comparison for microbial diversity fingerprinting

et al. 2019

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MultiLocus Sequence Analysis- and Amplified Fragment Length Polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species

Cited by 42 publications

References 39 publications

Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

Prevalence of HPV and variation of HPV 16/HPV 18 E6/E7 genes in cervical cancer in women in South West China

AFLP protocol comparison for microbial diversity fingerprinting

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