Pan-genomics of plant pathogens and its applications

Amir, Rabia; Sani, Qurat-ul-Ain; Maqsood, Wajahat; Munir, Faiza; Fatima, Nosheen; Siddiqa, Amnah; Ahmad, Jamil

doi:10.1016/b978-0-12-817076-2.00006-8

Cited by 5 publications

(8 citation statements)

References 113 publications

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“…The pangenomes of plant pathogens are often associated with species- or strain-specific virulence, host specificity or adaptive potential, or evolutionary history ( Amir et al, 2020 ). To investigate the genomic plasticity of genus Pectobacterium , the 64 complete genomes from 9 Pectobacterium spp.…”

Section: Resultsmentioning

confidence: 99%

“…Comparative genomics, including pangenome analysis, has also been used to reveal the basis of pathogenicity, genomic diversity, pathogenic evolution and host adaptation ( Toth et al, 2006 ; Sheppard et al, 2018 ; Amir et al, 2020 ). For Pectobacterium spp., genome-wide analyses have indicated considerable variation in the pathogenicity determinants including phytotoxins, polysaccharides, iron uptake systems, asecretion systems (type IV-VI), antimicrobial compounds, and CRISPR-Cas systems, whereas the plant cell wall degrading enzymes (PCWDEs) are highly conserved ( Li et al, 2018 , 2019 ; Arizala and Arif, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Zhang

Chu

et al. 2022

Front. Microbiol.

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Zhang

Chu

et al. 2022

Front. Microbiol.

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“…The single reference genome cannot reflect the genetic diversity of a species. Therefore, the pan-genome concept has been proposed and used to study various organisms [ 131 ]. This concept was first adopted to study Streptococcus agalactiae , a human bacterial pathogen causing neonatal infection, with the aim to explore the intraspecies gene variability [ 132 ].…”

Section: Future Perspectivesmentioning

confidence: 99%

“…[ 17 ] and Zymospetoria tritici [ 133 ]. Due to the relatively large genome size of fungal pathogens compared to bacteria, the pan-genomes of only a few fungi are available [ 131 ]. In fact, the PGTAus pan-genome database of Pgt is only one pan-genome available in the cereal rust fungi [ 59 ].…”

Section: Future Perspectivesmentioning

confidence: 99%

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Current Status and Future Perspectives of Genomics Research in the Rust Fungi

Xia

Qiu

Wang

et al. 2022

IJMS

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Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.

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