Research area · phylogenomics

Phylogenomics of Streptomyces silvae

Genome-based phylogenetic reconstruction places the analyzed strains within a coherent S. silvae lineage while revealing clear internal branching and evolutionary diversification.

This page summarizes TYGS- and GBDP-based phylogenomics and shows how genome-scale tree reconstruction supports both species-level assignment and strain-level differentiation within the clade.

Key findings Jump to phylogenetic tree

Key findings

Coherent lineage

All analyzed strains cluster within a coherent S. silvae lineage in the genome-based phylogenetic reconstruction.

Internal branching

The tree shows clear internal structure, indicating evolutionary differentiation within the species rather than complete genomic uniformity.

Closest genome pair

Streptomyces sp. LamerLS–316 and SID4921 group tightly together, consistent with their exceptionally high genome similarity.

Phylogenomics supports taxonomy

The phylogenomic reconstruction reinforces species-level assignment while providing higher-resolution insight into relationships within the clade.

Tree reconstruction

Phylogenetic reconstruction was based on GBDP distances calculated from whole-genome sequences. Tree inference was performed with FastME, and branch support values were estimated from 100 pseudo-bootstrap replicates.

Method

Genome BLAST Distance Phylogeny (GBDP) as implemented in the TYGS platform.

Tree inference

FastME reconstruction with branch lengths scaled according to the GBDP distance formula d5 and support values from 100 replicates.

Phylogenetic tree

The resulting genome-based tree provides a clade-level overview of relatedness and branching structure across the analyzed strains.

Phylogenetic tree of Streptomyces silvae strains
Figure 1. Genome-based phylogenetic tree of the S. silvae dataset based on GBDP distances. Branch lengths are scaled according to the GBDP distance formula d5, and node values indicate pseudo-bootstrap support from 100 replicates.
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Tree-level conclusion

The topology supports assignment of all analyzed genomes to the same species framework while retaining visible internal differentiation.

Most closely grouped strains

The tight grouping of LamerLS–316 and SID4921 mirrors their extremely high similarity in ANI-based comparisons.

The phylogenomic tree shows that the S. silvae clade is genomically coherent but not homogeneous. Some strains form very tight subclusters, whereas others occupy more distinct positions within the lineage, reflecting evolutionary diversification within the species rather than taxonomic separation.