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Fig. S1 Amino acid alignment of selected fungal MATA-HMG and their resulting phylogenetic reconstruction.

Fig. S2 Amino acid alignment of HMG49 showing the conservation of polymorphisms in isolates from broad geographical locations and trans-species polymorphisms.

Fig. S3 Amino acid alignment of HMG37 showing the conservation of polymorphisms among isolates of R. irregularis of a broad geographical origin.

Fig. S4 Amino acid alignment of HMG47 showing the conservation of polymorphisms among isolates of R. irregularis of a broad geographical origin.

Fig. S5 Polymorphisms conserved across isolates from broad geographical regions at HMG61.

Fig. S6 Amino acid alignment of HMG51 showing the conservation of polymorphisms among isolates of R. irregularis of a broad geographical origin.

Fig. S7 Amino acid alignment of HMG45 showing trans-species polymorphisms between an isolate of R. diaphanus and isolates of R. irregularis.

Fig. S8 Phylogenetic incongruence for regions of the HMG6, HMG7 and HMG49 genes.

Fig. S9 PCR evidence for the presence of specific alleles for the gene HMG6.

Fig. S10 Abundance of the MATA-HMG domain, compared with other genes previously reported to be very variable in R. irregularis; POL1-like and Hsp70.

Table S1 List of primers used for PCR, IPCR and RT-QPCR methods in this study

Table S2 Twenty-five fungal MATA_HMG representatives used as query sequences in the survey of AMF transcriptomes