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The commentary by Malar et al. [1] raised four criticisms of our study [2]. (1) Observed upregulated genes were not the closest orthologs of genes involved in mating in other fungi. (2) Reanalysis of RNA-seq data failed to detect upregulation of 18 R. irregularis genes during co-existence of two R. irregularis isolates in cassava. (3) An adjusted probability of <0.1 led to a substantial number of false positives. (4) There was no evidence that two R. irregularis isolates showed divergence in a putative MAT-locus indicating mating compatibility. We consider that there are serious errors in the assumptions and rationale used for the reanalyses, a mis-interpretation of the original data, as well as the discarding of important data without any justification.

Co-existence of AMF with different putative MAT-alleles induces genes homologous to those involved in mating in other fungi: a reply to Malar et al.