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

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.

Fig 1. Structure of the genome assembly.

Fig 2. Venn diagram of genes common to Pandoraea sp. 892iso and the four other Pandoraea types.

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. 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. 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. Phylogenetic tree of ppnI and ppnR.

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.