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[Preprint]. 2023 Dec 20:2023.12.20.572574. [Version 1] doi: 10.1101/2023.12.20.572574

Figure 1: Host phylogeny of S. paradoxus annotated with estimated Ty4/Tsu4 copy number.

Figure 1:

(A) Midpoint rooted ML phylogenetic tree of 370 S. paradoxus strains integrated from multiple public short-read WGS datasets (see Materials and Methods). Bootstrap support is annotated for key nodes. Major lineages and sub-lineages are annotated according to previously-reported population structure (Eberlein et al., 2019; He et al., 2022). The N. American strain DG1768 used in retromobility studies (Chen et al., 2022b) is found in the SpB sub-lineage and is indicated by the circled number 1. The S. American strain UFRJ50916 is found in the SpB sub-lineage and is indicated by the circled number 2. The Hawaiian strain UWOPS91-917.1 is found in its own sub-lineage indicated by the circled number 3. (B) Copy number estimates for the Ty4 subfamily. (C) Copy number estimates for the Tsu4 subfamily. In (B) and (C), gray bars represent copy number estimates for LTRs, whereas black bars represent estimated copy number for internal regions.