Table 1.
Genome features of the four consortium marine strains and the reference assemblies for comparative genomic analysis.
The consortium genome features are marked in gray.
Fig 1.
Phylogenetic reconstruction using the 92 marker genes extracted with the UBCG tool for prokaryotes.
The tree was constructed using the maximum likelihood method with IQ-TREE and was based on 1,000 ultrafast bootstrap replicates. The obtained substitution model was TIM+F+R10. Clades corresponding to the four genera of the consortium genomes, namely Alloalcanivorax (orange), Halopseudomonas (yellow), Paenarthrobacter (pale blue), and Pseudomonas (dark blue), are highlighted. The consortium genomes are denoted in bold with a red star, and the origin of each strain is shown with colored squares.
Fig 2.
Comparison of syntenic blocks between consortium genomes and complete reference genomes using the Sibelia tool with default parameters.
(A) Alloalcanivorax xenomutans GOM8 vs. A. xenomutans P40. (B) Halopseudomonas aestusnigri GOM5 vs. Halopseudomonas sp. MFKK-1. (C) Paenarthrobacter sp. GOM3 vs. Paenarthrobacter nicotinovorans ATCC 49919. (D) Pseudomonas aeruginosa GOM9 vs. P. aeruginosa DSM 50071. From the outermost ring to the center, the content is as follows: Each pair of genomes is marked in blue and purple, the size of each genome is indicated with gray numbers, the contigs of each genome are marked in pale green (darker green contigs indicate a positive direction, while red indicates a negative direction of the sequences), and different colors represent the syntenic blocks.
Fig 3.
KEGG functional and secondary metabolite-related gene cluster (SMGC) predictions for the consortium bacterial genomes.
(A) Comparison between the KO markers on level 2 of the KEGG functional category. The total gene numbers are in blue, unique or nonshared KOs in red, and the shared KO counts or the intersection for all four genomes in orange. The more intense colors observed in the P. aeruginosa GOM9 genome in the first panel, in contrast to the other three, are consistent with its larger genome size. (B) UpSet plot with the number of shared and nonshared KOs. (C) Heatmap with the SMGCs predicted with the antiSMASH software in ‘strict’ mode.
Fig 4.
Genes related to the aerobic HC degradation of alkanes and aromatics.
The functional prediction was made using the HADEG database and the RAST-tk annotation.
Fig 5.
Gain and loss of orthologous genes in the consortium and their relatives of the genomes selected for phylogenomic inference.
(A) Total protein families. The circles represent the gain (green), losses (orange), and no gains/losses (gray) in each node. (B) Protein families related to HC degradation and biosurfactant production. The HCs are shown as circles (alkanes) and squares (aromatics), and the biosurfactants are shown as triangles.