Fig 1.
Pan-genome structure and function of type strains of Nocardia.
(A) Gene accumulation curves for the pan-genome. (B) Gene accumulation curves for the core genome. The cumulative sizes of the pan-genome and core genome were calculated by type strains without replacement in random order 1000 times and then used to calculate the mean size. Error bars indicate one standard deviation from the mean. Five synonymous species were removed as described in Fig 2 and Table 1. (C) Distribution of functional categories in Nocardia core, accessory, and unique genomes and horizontal genes. (D) The number of gene families in each gene set. (E) The 20 potential donor bacterial genera providing donor genes for HGT. (F) Distribution of horizontal genes acquired in Nocardia spp.
Fig 2.
Phylogenomic and phylogenetic trees of the type strains of Nocardia.
(A) A phylogenomic tree was constructed based on the concatenation of 384 single-copy genes from 86 type strains. The isolated source, pathogenicity, and geographical origin are shown. (B) Phylogenetic tree based on the single gene dapb1 from 86 type strains. Each tree was constructed by the maximum likelihood method with 1000 bootstrap replicates. Rhodococcus globerulus NBRC 14531 served as an outgroup. Bootstrap values are indicated on the nodes. The colored branches indicate the five main phylogenetic groups. Black boxes indicate synonymous species.
Fig 3.
Heatmap of pairwise ANI and isDDH values for 86 type strains.
(A) Species delineation at an ANI threshold of 96% and (B) isDDH threshold of 70%. The isolate names on the left are the same as those in Fig 2A with the outgroup removed. The values underlying this heatmap were provided in the S4 and S5 Tables.
Table 1.
Inconsistent species assignment of strains in the genus Nocardia.
Table 2.
General features of novel species.
Fig 4.
Phylogenomic tree of members of the genus Nocardia.
A maximum-likelihood phylogeny tree was built based on the concatenation of 298 single-copy genes from 81 type strains and 28 putative new species with 1000 bootstrap replicates. The genome of Rhodococcus globerulus NBRC 14531 was included as an outgroup. Phylogenetic groups are highlighted in different colors.