Genetic diversity of Xanthomonas axonopodis pv. citri based on plasmid profile and pulsed field gel electrophoresis

Carvalho, Flávia Maria de Souza; Caramori, Lázara Pereira Campos; Júnior, Rui Pereira Leite

doi:10.1590/s1415-47572005000300020

Cited by 10 publications

(6 citation statements)

References 19 publications

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“…The variable plasmid configuration, that we observed in Xc-A strains in this study, was also previously reported by Amuthan & Mahadeban [ 32 ], and Carvalho et al [ 9 ]. Recently, it was determined in specific strains of Pseudomonas syringae pv.…”

Section: Discussionsupporting

confidence: 90%

“…However, plasmid variation was not considered in their study. In 2005, Carvalho et al [ 9 ] characterized the genetic diversity of 22 X. citri A-type strains from South America. Based on the comparison of plasmid profiles, and based on RFLPs identified via pulsed-field-gel electrophoresis, the authors observed high coefficients of similarity for strains isolated in similar geographical locations (from 0.83 to 1 for strains isolated in seven Brazilian states and between 0.62 and 0.83 for strains from Argentina, Bolivia, Paraguay and Uruguay).…”

Section: Introductionmentioning

confidence: 99%

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Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

et al. 2018

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BackgroundXanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains.ResultsWe utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs. Due to the intriguing nature of this pathogenicity plasmid with Tn3-like transposon association, repetitive elements and multiple putative sites for origins of replication, we might expect alternative structures of this plasmid in nature, illustrating the strong adaptive potential of X. citri strains. Analysis of the pathogenicity plasmid among completely sequenced X. citri strains, coupled with Southern hybridization of the pathogenicity plasmids, revealed clues to rearrangements of plasmids and resulting reshuffling of TALEs among strains.ConclusionsWe demonstrate in this study the importance of long-read sequencing for obtaining intact sequences of TALEs and plasmids, as well as for identifying rearrangement events including plasmid reshuffling. Rearrangement events, such as the hybrid plasmid in this case, could be a frequent phenomenon in the evolution of X. citri strains, although so far it is undetected due to the inability to obtain complete plasmid sequences with short-read sequencing methods.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4408-9) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

et al. 2018

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“…Important reasons for the lack of knowledge are due to the great genetic variability of phytopathogens as the X. fastidiosa and Xanthomonas spp., the slow-growth of the fungus P. citricarpa and ineffective tentatives in culturing the bacterium Candidatus Liberibacter spp. Therefore, these challenges require deeper biochemical and chemical studies (Carvalho et al, 2005;Nunney et al, 2014;Frare et al, 2019;Merfa et al, 2019).…”

Section: Final Remarks and Future Perspectivesmentioning

confidence: 99%

An overview of the most threating diseases that affect worldwide citriculture: Main features, diagnose, and current control strategies

et al. 2023

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Citriculture has been one of the most important agricultural activities worldwide. Brazil is among the five major citrus producers in the world, together with China, the European Union (EU), the United States, and Mexico. Together, these five groups are responsible for about 50% of the global citrus fruit production and this industrial segment is responsible for generating direct and indirect jobs. However, several citric diseases such as citrus canker, huanglongbing, citrus variegated chlorosis, and citrus black spot have been associated with annual losses of tons of fruits and orange trees impacting the global economy for decades. Citrus canker is caused by the Gram-negative bacteria Xanthomonas citri subsp. citri. and is associated with symptoms such as the formation of chlorotic rings in the leaves, stems, and fruits. Huanglongbing (HLB) is mainly associated with the Gram-negative bacteria Candidatus Liberibacter spp. and its main symptoms are the appearance of yellowish branches and deformed small leaves with yellowish spots. Citrus variegated chlorosis (CVC) is associated with the bacterium Xylella fastidiosa and causes chlorotic spots with irregular edges on leaves and deformation of new leaves. Citrus black spot (CBS) is caused by the fungus Phyllosticta citricarpa and generates lesions on fruits and reddish-brown leaf lesions. Since citrus is important for global agriculture, the current review addresses the main features of these important diseases including their symptoms and transmission, as well as the diagnosis and control strategies that have been studied so far for application in the field.

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“…A relatively high amount of genetic diversity was observed among isolates, indicating that there might be distinct pathotypes of the bacterium present in Malaysia. Carvalho et al (2005) investigated X. axonopodis pv. citri strains by pulsed-field and plasmid profile analysis.…”

Section: Morphological Characteristics Of Isolated X Axonopodis Pv Citrimentioning

confidence: 99%

Morpho-Molecular Characterization of Xanthomonas Axonopodis Pv. Citri Associated with Kinnow (Mandarin) and its Management

Iqbal¹,

Ehetisham-ul-Haq²,

Kamran³

et al. 2021

PJAR

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K innow (Citrus reticulata) belongs to the genus "Citrus" and the family "Rutaceae" is an important fruit around the globe (Penjor et al., 2013). It is used as fresh or in processed form like squashes, jams or pickles. Citrus fruit is rich in vitamin C, sugar, citric acid (Economos and Clay, 1999), and have valuable medicinal properties like prevention from hypothermia, malaria and to facilitate blood coagulation (Benavente-

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Genetic diversity of Xanthomonas axonopodis pv. citri based on plasmid profile and pulsed field gel electrophoresis

Cited by 10 publications

References 19 publications

Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

An overview of the most threating diseases that affect worldwide citriculture: Main features, diagnose, and current control strategies

Morpho-Molecular Characterization of Xanthomonas Axonopodis Pv. Citri Associated with Kinnow (Mandarin) and its Management

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