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Volume 6, Issue 10

Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Open Access

Abstract

is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 . isolates with isolation time spanning an 80‐year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of dates back to ~80 000 years ago. We showed that the pangenome of the 173 . strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that shared its 11 ARGs with 55 different bacterial species, and a high frequency of ARG transfer may have occurred between and species in the genera and . Correlation analysis showed that the ARG number in strains increased with time, while the virulence gene number was relative stable. Our results, taken together with previous studies, revealed the high genome openness and genetic diversity of and provide a comprehensive view of the phylogeny, genomic features, virulence gene and ARG profiles of worldwide strains.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antibiotic Resistance Gene , Clostridium perfringens , Openness Index , Phylogenetic Tree and Toxins
Funding
This study was supported by the:
  • Starting Grants program for young talents in China Agricultural University
    • Principle Award Recipient: Yongfei Hu
  • National Key Research and Development Program of China under Grant (Award 2018YFD0500505)
    • Principle Award Recipient: Xuezheng Fan
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2024-04-19
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Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens
M Gen 6, e000441 (2020); https://doi.org/10.1099/mgen.0.000441
/content/journal/mgen/10.1099/mgen.0.000441
/content/journal/mgen/10.1099/mgen.0.000441
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