Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Salzberg, Steven L.; Sommer, Daniel; Schatz, Michael C.; Phillippy, Adam M.; Rabinowicz, Pablo D.; Tsuge, Seiji; Furutani, Ayako; Ochiai, Hirokazu; Delcher, Arthur L.; Kelley, David R.; Madupu, Ramana; Puiu, Daniela; Radune, Diana; Shumway, Martin; Trapnell, Cole; Gudlur, Aparna; Jha, Gopaljee; Pandey, Alok; Patil, Prabhu B.; Ishihara, Hisashi; Meyer, Damien; Szurek, Boris; Verdier, Valérie; Koebnik, Ralf; Dow, J. Maxwell; Ryan, Robert P.; Hirata, Haruyuki; Tsuyumu, Shinji; Lee, Sang Won; Ronald, Pamela C.; Sonti, Ramesh V.; Sluys, Marie‐Anne Van; Leach, Jan E.; White, Frank F.; Bogdanove, Adam J.

doi:10.1186/1471-2164-9-204

Cited by 325 publications

(234 citation statements)

References 66 publications

(73 reference statements)

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“…oryzae and strain BLS256 for X. oryzae pv. oryzicola (11,12,14,32). Nontarget bacterial DNAs were pooled in equimolar concentrations, with the DNA from 10 strains included in each pool.…”

Section: Methodsmentioning

confidence: 99%

“…oryzae and two strains of X. oryzae pv. oryzicola are publicly available (GenBank accession numbers AYSX00000000 and AYSY00000000, respectively) (11)(12)(13)(14). These resources, along with draft genome sequences of another nine X. oryzae strains, provided insights into the genetic diversity among strains within this species, including a unique group of weakly pathogenic X. oryzae strains isolated in the United States (13; V. Verdier, unpublished).…”

mentioning

confidence: 99%

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Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Lang

Langlois

Nguyen

et al. 2014

Appl Environ Microbiol

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dMolecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10 4 to 10 5 CFU ml ؊1 , while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.

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“…oryzae and strain BLS256 for X. oryzae pv. oryzicola (11,12,14,32). Nontarget bacterial DNAs were pooled in equimolar concentrations, with the DNA from 10 strains included in each pool.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Lang

Langlois

Nguyen

et al. 2014

Appl Environ Microbiol

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“…3B). In addition to the numerous regulatory loci that map elsewhere in the Xanthomonas genomes (16)(17)(18)(19)(20), our findings highlight the existence of key regulatory loci that map within the hrp-hrc-hpa genes in X. oryzae pv. oryzicola.…”

Section: Discussionmentioning

confidence: 94%

“…In xanthomonads, the hrp-hrc-hpa genes are highly conserved and clustered within several sequenced genomes (16)(17)(18)(19)(20). Our previous studies revealed that the hrp cluster in X. oryzae pv.…”

mentioning

confidence: 99%

HrcT Is a Key Component of the Type III Secretion System in Xanthomonas spp. and Also Regulates the Expression of the Key hrp Transcriptional Activator HrpX

Liu

Zou

Xue

et al. 2014

Appl Environ Microbiol

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The type III secretion system (T3SS), encoded by hrp (hypersensitive response and pathogenicity) genes in Gram-negative phytopathogenic bacteria, delivers repertoires of T3SS effectors (T3SEs) into plant cells to trigger the hypersensitive response (HR) in nonhost or resistant-host plants and promote pathogenicity in susceptible plants. The expression of hrp genes in Xanthomonas is regulated by two key regulatory proteins, HrpG and HrpX. However, the interactions between hrp gene products in directing T3SE secretion are largely unknown. Here we demonstrated that HrcT of X. oryzae pv. oryzicola functions as a T3SS component and positively regulates the expression of hrpX. Transcription of hrcT occurs via two distinct promoters; one (T1) is with the hrpB operon and the second (T3) within hrpB7 Via either promoter T1 or T3, the defect in Hrp phenotype by hrcT deletion was corrected in the presence of hrcT only from Xanthomonas species but not from other phytopathogenic bacteria. An N-terminally truncated HrcT was able to bind the hrpX promoter and activate the expression of hrpX, supporting that HrcT is a positive regulator of hrpX. A revised model showing the regulatory interactions between HrcT, HrpX, and HrpG is proposed.

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“…citri, X. campestris pv. campestris, Xanthomonas perforans have been documented (Kim et al, 2009;Lee et al, 2005;Ochiai et al, 2005;Salzberg et al, 2008), only a few of them have been studied extensively for their functional role in disease induction (AkimotoTomiyama et al, 2012;Bartetzko et al, 2009;Kim et al, 2009;Kumar and Mondal, 2013;Mondal et al, 2016;Song and Yang, 2010). The Indian Xoo strain has been studied recently in details for their composition of T3SS effectors.…”

Section: Discussionmentioning

confidence: 99%

Dialogue between Xop-T3SS Effectors of <I>Xanthomonas oryzae Pv. Iryzae</I> and Rice during Bacterial Blight Pathogenesis

Mondal¹

2017

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Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major biotic threat to rice production globally. Xoo initiates dialogue with rice plant through its effectors that are secreted via type 3 secretion system (referred to as T3SS effectors). The result of this dialogue leads to the phenotype of either susceptible or resistance reaction. Xoo secrets two type of T3SS effectors, Xop (Xanthomonas outer protein) and TAL (Transcription activator like) effectors. Screened the total composition of T3SS effectors in one of the most virulent Xoo race 4 from India. Xoo race4 contains 21 Xop and 18 TAL effectors. This paper discusses recent insight into the dialogue between Xop T3SS and rice. Studied inducible, hrpdependent expression pattern of the Xop T3SS effectors. We created null mutants for each Xop T3SS effectors to understand their function in blight induction. Our subsequent investigation revealed that major Xop T3SS effectors like XopF, XopR plays crucial role during blight pathogenesis. The major effectors regulate the in planta Xoo growth and suppress PAMPtriggered immune (PTI) response in rice. Though there was no aberration in phenotypic as well as in vitro growth characters between wild and mutants, but mutants showed significant reduction during in planta colonization relative to the wild strain. The RT-qPCR analysis indicated significant fold increase in expression of the PTI marker genes in rice upon challengeinoculation with mutants suggesting the role of effectors in suppressing rice PTI. It is evident that mutants induced more callose deposition in infected rice leaves. When transiently expressed in Nicotiana benthamiana, fusion effector gene products get localized to the plasma membrane. Collectively, our insight into the Xop T3SS effectors leads to the understanding that the major T3SS effectors like XopF, XopR suppress rice immune responses, and thereby favours Xoo for its in planta growth and pathogenicity during bacterial blight development.

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Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Cited by 325 publications

References 66 publications

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

HrcT Is a Key Component of the Type III Secretion System in Xanthomonas spp. and Also Regulates the Expression of the Key hrp Transcriptional Activator HrpX

Dialogue between Xop-T3SS Effectors of <I>Xanthomonas oryzae Pv. Iryzae</I> and Rice during Bacterial Blight Pathogenesis

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