Data repository established for the appendix dataset documented in Scarlet M. Au’s MPhil in Biological Science (Plant Sciences) thesis, submitted to the University of Cambridge, UK. Appendix A. List of 182 species from the Mucoromycota subphylum Appendix B. List of 535 BUSCO single copy genes identified for single copy phylogenies. 1) Appendix B-1 contains BUSCO genes mostly annotated relative to the Rhizophagus irregularis DAOM_181602_v1.0. For genes that were missing, annotations were drawn from the Lyc-1 and the Thamnidium elegans genomes. 2) Appendix B-2 contains BUSCO genes annotated relative to the Rhizophagus irregularis DAOM_181602_v1.0 genome. 3) Appendix B-3 contains BUSCO genes annotated relative to the Lyc-1 genome. 4) Appendix B-4 contains BUSCO genes annotated relative to the Thamnidium elegans genome. Appendix C. Hierarchical clustering by orthogroup absence/presence and abundance. 1) Full hierarchical clustering by row (species) and columns (orthogroups) for binary matrix. 2) Full hierarchical clustering by row (species) and columns (orthogroups) for normalised matrix. 3) Full hierarchical clustering by row (species) only for binary matrix. 4) Full hierarchical clustering by row (species only) for normalised matrix. Appendix D. 36 out of 72 orthogroups shared between MFRE and AM fungal genomes contain known functional annotations.