Bioinformatic analysis of the complete genome sequence of Pectobacterium carotovorum subsp. brasiliense BZA12 and candidate effector screening

Huang, Yufei; Liu, Changyuan; Wang, Hui; Guan, Tianshu; Liu, Li; Yu, Shuyi

doi:10.1007/s42161-018-0126-7

Cited by 9 publications

(9 citation statements)

References 39 publications

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“…brasiliense and reported pan and core genome sizes of 6065 and 3264, respectively. In a recent study conducted in 2018 [24], compared P. c. subsp. carotovorum, P. c. subsp.…”

Section: Discussionmentioning

confidence: 99%

“…Putative genes that promote specific interactions between bacteria and their cognate plant hosts have also been uncovered by using comparative genomics approaches [35]. To date, few comparison studies have been conducted regarding Pectobacterium [8,24,27,39]. However, none of them have compared the virulence mechanisms, antimicrobial gene clusters, and the diversity of the immune system clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) across all species that currently comprise the Pectobacterium genus in detail.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium

Arizala

Arif

2019

Pathogens

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The Pectobacterium genus comprises pectolytic enterobacteria defined as the causal agents of soft rot, blackleg, and aerial stem rot diseases of potato and economically important crops. In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. odoriferum was shown to harbor numerous pseudogenes, which suggests low coding capacity and genomic degradation. The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. The analyses unveiled a noteworthy heterogeneity in the pathogenicity determinants. Specifically, phytotoxins, polysaccharides, iron uptake systems, and the type secretion systems III–V were observed in just some species. Likewise, a comparison of gene clusters encoding antimicrobial compounds put in evidence for high conservation of carotovoricin, whereas a few species possessed the phenazine, carbapenem, and carocins. Moreover, three clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems: I-E, I-F, and III-A were identified. Surrounding some CRISPR-Cas regions, different toxin and antitoxin systems were found, which suggests bacterial suicide in the case of an immune system failure. Multiple whole-genome alignments shed light on to the presence of a novel cellobiose phosphotransferase system (PTS) exclusive to P. parmenteri, and an unreported T5SS conserved in almost all species. Several regions that were associated with virulence, microbe antagonism, and adaptive immune systems were predicted within genomic islands, which underscored the essential role that horizontal gene transfer has imparted in the dynamic evolution and speciation of Pectobacterium species. Overall, the results decipher the different strategies that each species has developed to infect their hosts, outcompete for food resources, and defend against bacteriophages. Our investigation provides novel genetic insights that will assist in understanding the pathogenic lifestyle of Pectobacterium, a genus that jeopardizes the agriculture sustainability of important crops worldwide.

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“…brasiliense and reported pan and core genome sizes of 6065 and 3264, respectively. In a recent study conducted in 2018 [24], compared P. c. subsp. carotovorum, P. c. subsp.…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium

Arizala

Arif

2019

Pathogens

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“…are considered to be broad-host range pathogens, except that P. atrosepticum and P. parmentieri have been reported almost exclusively from potatoes ( Solanum tuberosum ) and P. betavasculorum almost exclusively from sugar beets ( Beta vulgaris ). The taxonomic position of many strains in the Pectobacterium genus has been re-classified in recent years [2, 9, 10]. For example, Pcc PC1 was classified into P. aroidearum , and P. peruviense , P. polaris and Candidatus P. maceratum were separated from P. carotovorum.…”

Section: Discussionmentioning

confidence: 99%

“…pekinensis [2] and P. carotovorum subsp. brasiliense BZA12 isolated from Cucumis sativus [9], P. carotovorum subsp. odoriferum BC S7 isolated from Brassica rapa ssp.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of Pectobacterium carotovorum subsp. brasiliense SX309 provides novel insights into its genetic and phenotypic features

Yuan

Shi

et al. 2019

BMC Genomics

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Background Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading enzymes is usually critical for Pectobacterium infection. However, other virulence factors and the mechanisms of genetic adaptation still need to be studied in detail. Results In this study, the complete genome of P. carotovorum subsp. brasiliense strain SX309 isolated from cucumber was compared with eight other pathogenic bacteria belonging to the Pectobacterium genus, which were isolated from various host plants. Genome comparison revealed that most virulence genes are highly conserved in the Pectobacterium strains, especially for the key virulence determinants involved in the biosynthesis of extracellular enzymes and others including the type II and III secretion systems, quorum sensing system, flagellar and chemotactic genes. Nevertheless, some variable regions of the T6SS and the CRISP-Cas immune system are unique for P. carotovorum subsp. brasiliense . Conclusions The extensive comparative genomics analysis revealed highly conserved virulence genes in the Pectobacterium strains. However, several variable regions of type VI secretion system and two subtype Cas mechanism-Cas immune systems possibly contribute to the process of Pectobacterium infection and adaptive immunity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5831-x) contains supplementary material, which is available to authorized users.

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“…Therefore, some genomic comparisons have also allowed for delineating taxa, for identifying the core repertoire of virulence genes shared by related organisms and, for locating gene clusters or genome islands exclusive of species or even unique of a strain for developing molecular tools for identification and detection of pathogens [ 23 ]. To date, few comparative studies have also been conducted regarding Pectobacterium species [ 24 , 25 , 26 , 27 , 28 ]. Until now, six Pbr complete genome sequences are publicly available: Pbr PCC21 (misnamed as P. carotovorum PCC21 in NCBI) isolated from B. rapa ssp.…”

Section: Genomics: From Advances In Taxonomy To Insights In Biodivmentioning

confidence: 99%

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

et al. 2021

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Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.

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Bioinformatic analysis of the complete genome sequence of Pectobacterium carotovorum subsp. brasiliense BZA12 and candidate effector screening

Cited by 9 publications

References 39 publications

Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium

Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium

Comparative genomic analysis of Pectobacterium carotovorum subsp. brasiliense SX309 provides novel insights into its genetic and phenotypic features

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

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