Whole genome sequencing and comparative genomics analysis of Pectobacterium carotovorum identifies key pathogenic genes

He, Xiaoliang; Lu, Tianhua; Zhou, Xiaohui

doi:10.1016/j.ympev.2021.107114

Cited by 8 publications

(9 citation statements)

References 50 publications

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“…Six Ppa strains, including type strains, also did not demonstrate T1SSa similar to HC, and three subsets have been identified in Pectobacterium species (Li et al, 2018). In other studies, P. aroidearum strain L6 showed 14 genes, and P. aroidearum strain PC1 demonstrated one gene (He et al, 2021;Xu et al, 2021). Further study on T1SS and protease secretion is required since Ppa strains, including HC with three T1SS, did not show protease activity in the medium (Jee et al, 2020).…”

Section: Cluster Of Orthologous Group Analysis Of South Koreanmentioning

confidence: 84%

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Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

et al. 2022

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In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.

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Section: Cluster Of Orthologous Group Analysis Of South Koreanmentioning

confidence: 84%

“… He et al (2021) conducted CAZyme analysis with Pca strain PC1, grouped in Par by Li et al (2018) . He et al (2021) identified 144 CAZymes, including 57 GHs, 35 GTs, 26 CEs, 15 PLs, and 8 AAs. The number of AAs and CEs in PC1 was higher than 1–2 in AAs and 8–12 in CEs in this study.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

et al. 2022

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“…Pectobacterium spp. has attracted more attention about its wide distribution and diversity (He et al, 2021). Pectobacterium usually exists in soils with a broad range of hosts; thus, Pectobacterium species cause soft rot disease in plants of at least 16 dicotyledonous and 11 monocotyledonous angiosperm families (Ma et al, 2007;Nabhan et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…At present, only strain PC1 of P. aroidearum has sequenced its whole genome (PC1 formerly classified as P. carotovorum subsp. carotovorum, the classification has not been corrected in the NCBI database; He et al, 2021). To understand the molecular mechanisms of taxonomy and pathogenic factors in P. aroidearum, the whole genome of L6 was successively sequenced in this study.…”

Section: Discussionmentioning

confidence: 99%

“…Pédron et al (2019) established the taxonomic status of six Pectobacterium strains based on phylogenetic data, ANI values, and isDDH results by comparative genomics and identified a novel species of the genus Pectobacterium named Pectobacterium aquaticum. He et al (2021) analyzed comparative genomics of four Pectobacterium strains and obtained three kinds of highly conserved key pathogenic genes related to cell-wall degrading enzymes in Pectobacterium strain PC1, including 19 pectinase genes, 25 cellulase genes, and 22 protease genes. Zhang et al (2016) compared 85 genomes of the genera Dickeya and Pectobacterium and found that at least ten tested genomes from these genera were misnamed in GenBank based on ANI, isDDH, and whole genome.…”

Section: Discussionmentioning

confidence: 99%

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Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics

Wang

Qin

et al. 2021

Front. Microbiol.

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Soft rot pectobacteria are devastating plant pathogens with a global distribution and a broad host range. Pectobacterium aroidearum L6, previously isolated from leaves of Syngonium podophyllum, is a pectolytic bacterial pathogen that causes typical soft rot on S. podophyllum. There is a shortage for genome data of P. aroidearum, which seriously hinders research on classification and pathogenesis of Pectobacterium. We present here the complete genome sequence of P. aroidearum L6. The L6 strain carries a single 4,995,896-bp chromosome with 53.10% G + C content and harbors 4,306 predicted protein-coding genes. We estimated in silico DNA–DNA hybridization and average nucleotide identity values in combination with the whole-genome-based phylogeny from 19 Pectobacterium strains including P. aroidearum L6. The results showed that L6 and PC1 formed a population distinct from other populations of the Pectobacterium genus. Phylogenetic analysis based on 16S rRNA and genome sequences showed a close evolutionary relationship among Pectobacterium species. Overall, evolutionary analysis showed that L6 was in the same branch with PC1. In comparison with 18 Pectobacterium spp. reference pathogens, strain L6 had 2,712 gene families, among which 1,632 gene families were identified as orthologous to those strains, as well as 1 putative unique gene family. We discovered 478 genes, 10.4% of the total of predicted genes, that were potentially related to pathogenesis using the Virulence Factors of Pathogenic Bacteria database. A total of 25 genes were related to toxins, 35 encoded plant cell-wall degrading enzymes, and 122 were involved in secretion systems. This study provides a foundation for a better understanding of the genomic structure of P. aroidearum and particularly offers information for the discovery of potential pathogenic factors and the development of more effective strategies against this pathogen.

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Genetic insights unraveling quorum quenching potential of indigenous isolates from an anaerobic membrane bioreactor

Waheed

Mehmood

et al. 2022

Science of The Total Environment

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Whole genome sequencing and comparative genomics analysis of Pectobacterium carotovorum identifies key pathogenic genes

Cited by 8 publications

References 50 publications

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics

Genetic insights unraveling quorum quenching potential of indigenous isolates from an anaerobic membrane bioreactor

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