Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics
Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequenc...
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| Format: | Article |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.868709/full |
| _version_ | 1818532625877303296 |
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| author | Yanan Zhang Honglong Chu Liqiong Yu Fei He Yong Gao Lizhou Tang |
| author_facet | Yanan Zhang Honglong Chu Liqiong Yu Fei He Yong Gao Lizhou Tang |
| author_sort | Yanan Zhang |
| collection | DOAJ |
| description | Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA–DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum. |
| first_indexed | 2024-12-11T17:47:59Z |
| format | Article |
| id | doaj.art-1e86f92378fa45ab8944c9d9db0a4e1f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T17:47:59Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-1e86f92378fa45ab8944c9d9db0a4e1f2022-12-22T00:56:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-07-011310.3389/fmicb.2022.868709868709Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative GenomicsYanan Zhang0Honglong Chu1Liqiong Yu2Fei He3Yong Gao4Lizhou Tang5College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, ChinaCollege of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, ChinaCollege of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, ChinaSchool of Modern Agriculture and Biotechnology, Ankang University, Ankang, ChinaCollege of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, ChinaCollege of Life Sciences, Jiangxi Normal University, Nanchang, ChinaBacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA–DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.https://www.frontiersin.org/articles/10.3389/fmicb.2022.868709/fullbacterial soft rotPectobacterium aroidearumcomparative genomicsgenomic rearrangementAmorphophallus konjac |
| spellingShingle | Yanan Zhang Honglong Chu Liqiong Yu Fei He Yong Gao Lizhou Tang Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics Frontiers in Microbiology bacterial soft rot Pectobacterium aroidearum comparative genomics genomic rearrangement Amorphophallus konjac |
| title | Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics |
| title_full | Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics |
| title_fullStr | Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics |
| title_full_unstemmed | Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics |
| title_short | Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics |
| title_sort | analysis of the taxonomy synteny and virulence factors for soft rot pathogen pectobacterium aroidearum in amorphophallus konjac using comparative genomics |
| topic | bacterial soft rot Pectobacterium aroidearum comparative genomics genomic rearrangement Amorphophallus konjac |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.868709/full |
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