Whole-Genome Sequences of Ralstonia solanacearum Strains P816, P822, and P824, Emerging Pathogens of Blueberry in Florida

Bocsanczy, Ana Maria; Espindola, Andres S.; Norman, David J.

doi:10.1128/mra.01316-18

Cited by 11 publications

(7 citation statements)

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“…A few research groups added a significant amount of host-compatibility information for a set of strains (Ailloud et al, 2015; Cho et al, 2018; Lebeau et al, 2011). Other groups have performed host-compatibility experiments and shared this information with us, for example, tobacco strain CQPS-1 (Liu et al, 2017) is also mildly pathogenic on tomato (Prof. W Ding, 2019, personal communication), while the blueberry strains P816, P822 and P824 (Bocsanczy, Espindola & Norman, 2019), are very aggressive on tomato (Dr. DJ Norman, 2019, personal communication). In our repertoire comparison, we allow a tolerance of presence for the Rip in the interval of strains between the total number of strains n , and n -5%, this allows to compensate the effect of unequal set of strains to compare.…”

Section: Discussionmentioning

confidence: 99%

“…These soil-resident bacteria are indeed important, as they affect many different plant species, ranging from solanaceous crops to other important crops like banana and peanut, in different parts of the world. Recently, new plant species have been found to be infected and present symptoms of bacterial wilt, like blueberry shrubs in Florida, USA (Bocsanczy, Espindola & Norman, 2019), ornamental roses in the Netherlands (Bergsma-Vlami et al, 2018), or pumpkin in China (She et al, 2017). This bacterium has one of the largest known repertoires of T3Es among all plant or animal pathogenic bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Pangenomic type III effector database of the plant pathogenicRalstoniaspp.

Sabbagh

Carrère

Lonjon

et al. 2019

PeerJ

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Background The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology). Methods Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors. Results We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pangenomic type III effector database of the plant pathogenicRalstoniaspp.

Sabbagh

Carrère

Lonjon

et al. 2019

PeerJ

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“…It is widely distributed throughout the world from tropical and subtropical regions to temperate and cool regions, possibly due to the global climate warming (Elphinstone et al, 2005; Jiang et al, 2017). Its multitudinous and increasing hosts incorporate quite a broad range of plant species, including both monocot and dicot, herbaceous and woody plants, such as tomato, potato, eggplant, peanut, ginger, banana, olive, mulberry, and geranium (Jiang et al, 2017; Bocsanczy et al, 2019). Thus, R. solanacearum is a major constraint to the production of several economically important agricultural crops and ornamental plants.…”

Section: Introductionmentioning

confidence: 99%

“…These genome data play an irreplaceable role in analyzing the genomic diversity and evolution within the R. solanacearum species complex, studying the genes contributing to host-range and characterizing the global regulation mechanisms that govern the bacterial virulence (Genin and Denny, 2012). Although plethora of genomes have been sequenced, more genome sequences are still needed to analyze the entire species, since new pathotypes are continuously isolated and identified (Bocsanczy et al, 2019). In addition, comparative genomic analysis has been widely used to identify genes contributing to virulence/hypovirulence or host specificity of a particular pathogen such as R. solanacearum (Gonzalez et al, 2011; Jalan et al, 2011, 2013; Siri et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer

Tan

Qiu

et al. 2019

Front. Microbiol.

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Ralstonia solanacearum , which causes bacterial wilt in a broad range of plants, is considered a “species complex” due to its significant genetic diversity. Recently, we have isolated a new R. solanacearum strain HA4-1 from Hong’an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel R. solanacearum effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on R. solanacearum species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in R. solanacearum to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between R. solanacearum and potato.

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“…Com os arquivos das sequências forward e reverse, eu montei as sequênciasconsenso com o programa Geneious (v. 8.0.5) (Bocsanczy et al, 2019;Fu et al, 2019;Nattier & Salazar, 2019;Bridgeman et al, 2020;Li et al, 2020), mantendo os parâmetros padrão do programa. No caso dos marcadores moleculares nucleares 18S e ITS2, diploides, eu utilizei a ferramenta virtual SeqPHASE (Flot, 2010) em conjunto com o programa PHASE (v.…”

Section: Iii4 Tratamento Das Sequências De Dna E Escolha Do Modelo De...unclassified

Sistemática e filogenia das espécies brasileiras de Mastigoproctus Pocock, 1894 (Arachnida: Uropygi: Mastigoproctinae)

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Em primeiro lugar, eu agradeço ao meu orientador, Ricardo, não apenas por sua orientação e pelas nossas discussões sobre o trabalho, mas pela amizade, confiança e atenção ao longo dos sete anos em que estou no laboratório, desde minha iniciação científica.Agradeço a minha namorada, Aline, não só pela companhia, paciência e incentivo, mas por ter aceitado a ideia de ir a uma coleta de campo e também por ter tido o cuidado de tirar fotos de ótima qualidade.Meu muito obrigado às pessoas que conheci no Laboratório de Aracnologia, alunos e ex-alunos. Ao Alípio e à Marília, por terem ido a coletas de campo. À Conchita e à Juliana, não apenas por terem participado de coletas de campo, mas pelos importantes comentários feitos para contribuir com a dissertação. Ao Jairo, por todos os conselhos e discussões a respeito do trabalho, e também por seus comentários, que com certeza contribuíram com a dissertação.Eu agradeço aos meus amigos da graduação Edgar "Véi", por ter aceitado coletar comigo, e Gabriel "Junior", pelo apoio, incentivo e pelas discussões de trabalho.Agradeço aos pesquisadores Antonio Brescovit, Rodrigo Ferreira, Amazonas Júnior e Renato Bérnils pelos empréstimos de material. Aos pesquisadores Luis Armas, Jason Dunlop, Fritz Geller-Grimm e Victor Krivokhatsky (in memoriam), pelas concessões de material fotográfico.Agradeço aos técnicos do Laboratório de Evolução Molecular, especialmente ao Manuel, pela paciência e ajuda nos procedimentos laboratoriais.Meu muito obrigado ao ex-coordenador do Programa de Pós-Graduação em Zoologia do IB-USP, Daniel Lahr, e ao atual coordenador, José Marian, por sempre estarem dispostos a ajudar e manter uma boa relação não só comigo, mas com todos os estudantes do departamento.Eu agradeço ao CNPq, pela concessão de bolsa de mestrado, e ao IB-USP, pela infraestrutura fornecida para a execução do trabalho.Finalmente, eu agradeço aos meus pais, Durval e Isabel, por todo o apoio, força e incentivo desde quando ingressei na graduação no IB-USP, oito anos atrás.

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Whole-Genome Sequences of Ralstonia solanacearum Strains P816, P822, and P824, Emerging Pathogens of Blueberry in Florida

Cited by 11 publications

References 5 publications

Pangenomic type III effector database of the plant pathogenicRalstoniaspp.

Pangenomic type III effector database of the plant pathogenicRalstoniaspp.

Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer

Sistemática e filogenia das espécies brasileiras de Mastigoproctus Pocock, 1894 (Arachnida: Uropygi: Mastigoproctinae)

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