Complete Genome Sequence Data of Four <i>Burkholderia glumae</i> Strains Isolated from Rice Fields in the United States

Lee, Hyun‐Hee; Lelis, Tiago; Ontoy, John; Bruno, Jobelle; Ham, Jong Hyun; Seo, Young-Su

doi:10.1094/mpmi-04-21-0090-a

Cited by 4 publications

(4 citation statements)

References 13 publications

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“…Once detected and characterized using the above approaches, six strains (60BGCRMSO1-5, 60BGCRMSO3-5, 60BGCRMSO3-9, 60BGCRMSO3-11, 60BGCRPA10-1, and 60BGCRWC8-5) were selected and subjected to whole-genome sequencing, characterization, and phylogenetic analysis. The genome characteristics of the sequenced strains were consistent with the previously sequenced strains of this pathogen (e.g., [20,21,32,33]), with a high level of completeness (Table 2). The toxoflavin gene cluster of the six genomes was identified and compared with the other publicly available B. glumae genomes.…”

Section: Discussionsupporting

confidence: 77%

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

et al. 2022

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Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen.

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Section: Discussionsupporting

confidence: 77%

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

et al. 2022

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“…The whole genome sequence information of the B. glumae strains 336gr-1 (virulent, non-pigmenting), 257sh-1 (avirulent, pigmenting), and 411gr-6 (hyper-virulent, pigmenting) was announced previously [16]. Their phenotypic traits are presented in Figure 1.…”

Section: Resultsmentioning

confidence: 99%

“…In that study, we identified hypervirulent, virulent, hypo-virulent, and naturally avirulent strains. Further, we sequenced the whole genomes of four strains representing different phenotypes in virulence and pigment production on CPG agar medium: 336gr-1 (virulent and non-pigment-producing), 411gr-6 (highly virulent and pigment-producing), 957856-41-c (hypo-virulent and non-pigment-producing), and 257sh-1 (avirulent and pigment-producing) [16].…”

Section: Introductionmentioning

confidence: 99%

qsmRencoding an IclR-family transcriptional factor is a core pathogenic determinant ofBurkholderia glumaebeyond the acyl-homoserine lactone-mediated quorum-sensing system

Lelis,

Bruno,

Padilla

et al. 2023

Preprint

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The plant pathogenic bacteriumBurkholderia glumaecauses bacterial panicle blight (BPB) in rice-growing areas worldwide. It has been widely accepted that an acyl-homoserine lactone (AHL)-type quorum sensing (QS) system encoded bytofIandtofRgenes (TofIR QS) is a key regulatory mechanism underlying the bacterial pathogenesis ofB. glumae. In addition,qsmR, which encodes an IclR-family regulatory protein, has been considered an important part of TofIR QS. However, the present study with three strains ofB. glumaerepresenting different pathogenic strains revealed that this currently accepted paradigm should be modified. We characterized the regulatory function of TofIR QS andqsmRin three different strains ofB. glumae, 336gr-1 (virulent), 411gr-6 (hypervirulent) and 257sh-1 (avirulent). In 336gr-1, both TofIR QS andqsmRwere critical for the pathogenesis, being consistent with previous studies. However, in the hypervirulent strain 411gr-6, TofIR QS only partially contributes to the virulence, whereasqsmRwas critical for pathogenesis like in 336gr-1. Furthermore, we found that a single nucleotide polymorphism causing T50K substitution in theqsmRcoding sequence was the cause of the non-pathogenic trait of the naturally avirulent strain 257sh-1. Subsequent analyses of gene expression and transcriptome revealed that TofIR QS is partially controlled byqsmRat the transcriptional level in both virulent strains. Further genetic tests of additionalB. glumaestrains showed that 11 out of 20 virulent strains retained the ability to produce toxoflavin even after removing thetofI/tofM/tofRQS gene cluster like 411gr-6. In contrast, all the virulent strains tested lost the function almost completely upon deletion of theqsmRgene. Taking these results together,qsmR, rather than TofIR QS, is a master regulator that determines the pathogenic trait ofB. glumaethus a more appropriate pathogen target for successful management of BPB.Author summaryBacterial cell-to-cell communication, called quorum-sensing, systems mediated by homoserine lactone (HSL)-type signaling molecules play pivotal roles in the virulence-related functions of diverse plant and animal pathogenic Gram-negative bacteria.Burkholderia glumaeis the chief causal agent for bacterial panicle blight, a devastating rice disease worldwide. In this pathogen, the HSL-type quorum-sensing system dependent on thetofIandtofRgenes had long been thought to be the core regulatory/signaling system essential for virulence. However, we discovered in this study that a highly virulent strain ofB. glumae, 411gr-6, retained its virulence even after thetofI/tofR-dependent quorum-sensing function was disabled. We also found that more than a half of the natural strains of this pathogen species tested in this study also exhibited their virulence function in the absence of thetofI/tofR-dependent quorum-sensing system. Then we characterized theqsmRgene as an essential regulatory/signaling element for the bacterial pathogenesis regardless of the genetic variations among the strains ofB. glumae. This study indicates that theqsmRgene, rather than thetofI/tofR-dependent quorum-sensing system, should be considered as an essential master regulatory/signaling factor for the virulence ofB. glumaeand, thus, a promising target for suppressing bacterial panicle blight.

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“…We sprayed with the bacterial suspension of B. glumae when panicles were emerging (20 to 30% emerged) from the boot at the booting stage. Empty seeds were calculated by cutting four rice ears from both processed and unprocessed plants (at the heading stage) to evaluate the empty seed rate [41]. The leaves of adult plants (2 months old) were inoculated with bacterial suspensions of Xoc.…”

Section: Pathogenicity Tests Of Parents and Offspringmentioning

confidence: 99%

Identification of QTLs Conferring Resistance to Bacterial Diseases in Rice

Fang

Degui

et al. 2023

Plants

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Bacterial panicle blight, bacterial leaf streak, and bacterial brown stripe are common bacterial diseases in rice that represent global threats to stable rice yields. In this study, we used the rice variety HZ, Nekken and their 120 RIL population as experimental materials. Phenotypes of the parents and RILs were quantitatively analyzed after inoculation with Burkholderia glumae, Xanthomonas oryzae pv. oryzicola, and Acidovorax avenae subsp. avenae. Genetic SNP maps were also constructed and used for QTL mapping of the quantitative traits. We located 40 QTL loci on 12 chromosomes. The analysis of disease resistance-related candidate genes in the QTL regions with high LOD value on chromosomes 1, 3, 4, and 12 revealed differential expression before and after treatment, suggesting that the identified genes mediated the variable disease resistance profiles of Huazhan and Nekken2. These results provide an important foundation for cloning bacterial-resistant QTLs of panicle blight, leaf streak, and brown stripe in rice.

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Complete Genome Sequence Data of Four Burkholderia glumae Strains Isolated from Rice Fields in the United States

Cited by 4 publications

References 13 publications

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

qsmRencoding an IclR-family transcriptional factor is a core pathogenic determinant ofBurkholderia glumaebeyond the acyl-homoserine lactone-mediated quorum-sensing system

Identification of QTLs Conferring Resistance to Bacterial Diseases in Rice

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