Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Aug 5;17(8):e0272435.
doi: 10.1371/journal.pone.0272435. eCollection 2022.

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

Rui-Fang Gao  1   2 , Ying Wang  1   2 , Ying Wang  1   2 , Zhi-Wen Wang  3 , Gui-Ming Zhang  1   2
Affiliations

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

Rui-Fang Gao et al. PLoS One. .

Abstract

In this study, we sequenced a bacteria isolate Pandoraea sp. 892iso isolated from a Phytophthora rubi strain which is an important plant pathogenic oomycete, identified through genome and combined the data with existing genomic data from other 28 the genus of Pandoraea species. Next, we conducted a comparative genomic analysis of the genome structure, evolutionary relationships, and pathogenic characteristics of Pandoraea species. Our results identified Pandoraea sp. 892iso as Pandoraea sputorum at both the genome and gene levels. At the genome level, we carried out phylogenetic analysis of single-copy, gene co-linearity, ANI (average nucleotide identity) and AAI (average amino acid identity) indices, rpoB similarity, MLSA phylogenetic analysis, and genome-to-genome distance calculator calculations to identify the relationship between Pandoraea sp. 892iso and P. sputorum. At the gene level, the quorum sensing genes ppnI and ppnR and the OXA-159 gene were assessed. It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Oomycetes strain of Phytophthora rubi.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Structure of the genome assembly.
Fig 2
Fig 2. Venn diagram of genes common to Pandoraea sp. 892iso and the four other Pandoraea types.
Fig 3
Fig 3. Phylogenetic analyses of the evolutionary relationships between Pandoraea sp. 892iso and Pandoraea types.
A neighbor-joining phylogenetic tree constructed based on single-copy genes common to these nine bacterial genomes. The neighbor-joining method was used in MEGA6, where a bootstrap test (1,000 replicates) is shown next to the branches.
Fig 4
Fig 4. Phylogenetic analyses of evolutionary relationships of ubiquitin genes among Pandoraea sp. 892iso and Pandoraea types.
A neighbor-joining phylogenetic tree constructed based on single-copy genes common to these nine bacterial genomes. The neighbor-joining method was used in MEGA6, where a bootstrap test (1,000 replicates) is shown next to the branches.
Fig 5
Fig 5. Phylogenetic tree highlighting the position of Pandoraea sp. 892iso relative to the other Pandoraea species.
The tree was aligned with the characteristics of the rpoB gene (a) and MLSA (b) under the maximum likelihood (ML) criterion.
Fig 6
Fig 6. Phylogenetic tree of ppnI and ppnR.
Fig 7
Fig 7. Phylogenetic tree of OXA-159 genes.
The neighbor-joining method was used in MEGA7, where a bootstrap test (1,000 replicates) is shown next to the branch.
See this image and copyright information in PMC

References

    1. Coenye T, Falsen E, Hoste B, Ohlén M, Goris J, Govan JR, et al.. Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. Int J Syst Evol Micr. 2000; 50(2):887–99. doi: 10.1099/00207713-50-2-887 - DOI - PubMed
    1. Schneider I, Queenan AM, Bauernfeind A. Novel carbapenem-hydrolyzing oxacillinase OXA-62 from Pandoraea pnomenusa. Antimicrob Agents Ch. 2006; 50(4):1330–5. doi: 10.1128/AAC.50.4.1330-1335.2006 - DOI - PMC - PubMed
    1. Stryjewski ME, LiPuma JJ, Messier RH Jr, Reller LB, Alexander BD. Sepsis, multiple organ failure, and death due to Pandoraea pnomenusa infection after lung transplantation. J Clin Microbiol. 2003; 41(5):2255–7. doi: 10.1128/JCM.41.5.2255-2257.2003 - DOI - PMC - PubMed
    1. Daneshvar MI, Hollis DG, Steigerwalt AG, Whitney AM, Spangler L, Douglas MP, et al.. Assignment of CDC weak oxidizer group 2 (WO-2) to the genus Pandoraea and characterization of three new Pandoraea genome species. J Clin Microbiol. 2001; 39(5):1819–26. doi: 10.1128/JCM.39.5.1819-1826.2001 - DOI - PMC - PubMed
    1. Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO, Kim YK, et al.. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int J Syst Evol Micr. 2010; 60(1):21–6. doi: 10.1099/ijs.0.012823-0 - DOI - PubMed

Publication types

Substances

Supplementary concepts