Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia
Fig 3
Pairwise phylogenetic branch lengths between homeologous gene pairs in tetraploid genomes.
(A) Histograms showing phylogenetic branch lengths (in amino acid substitutions per site) between homeologous gene pairs for tetraploid genomes. The relaxed branch length threshold for species delineation is highlighted in a dashed red line (0.032 amino acid substitutions per site). The percentage of gene pairs that exceed this same-species threshold is given in a box in the top right of each plot. (B) Oxford dot plot of tetraploid ilAceEphe1.ยต (from host Acentria ephemerella [Lepidoptera]) using BUSCO genes. Contig boundaries are marked by gray lines. Gene pairs that are less divergent than the same species threshold are in sky blue, while gene pairs that are more divergent than the same species threshold are in red. The data underlying (A) was generated by running BUSCO (microsporidia_odb10, version 5.4.6) [76] on the unpurged genome assemblies of the tetraploid genomes. For each tetraploid, the haplotypes of each BUSCO locus were aligned to one another and an outgroup using MAFFT (version 7.525) [90], and a phylogeny was generated for each alignment using IQ-TREE (version 2.3.4, with ModelFinder enabled) [77, 91]. Subsequently, the branch lengths between homeologous gene pairs were extracted from each phylogeny, and plotted in the histograms seen in (A) using a custom script in S1 Script. The individual BUSCO phylogenies used to derive this data can also be found in File Collection 15 at https://doi.org/10.5281/zenodo.17251512. The BUSCO gene annotations used to generate (B) can be found in File Collection 5 at https://doi.org/10.5281/zenodo.17251512. The figure was generated using Matplotlib [92], and manually annotated using InkScape (version 1.2.2).