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Background  The cyclic peptide toxins of  Amanita  mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in  Amanita bisporigera , and several other members are known from other species of  Amanita . However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains unknown.    Results  Draft genome sequences of two cyclic peptide-producing mushrooms, the “Death Cap”  A. phalloides  and the “Destroying Angel”  A. bisporigera , were obtained. Each species has ~30 MSDIN genes, most of which are predicted to encode unknown cyclic peptides. Some MSDIN genes were duplicated in one or the other species, but only three were common to both species. A gene encoding cycloamanide B, a previously described nontoxic cyclic heptapeptide, was also present in  A. phalloides , but genes for antamanide and cycloamanides A, C, and D were not. In  A. bisporigera , RNA expression was observed for 20 of the MSDIN family members. Based on their predicted sequences, novel cyclic peptides were searched for by LC/MS/MS in extracts of  A. phalloides . The presence of two cyclic peptides, named cycloamanides E and F with structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated. Of the MSDIN genes reported earlier from another specimen of  A. bisporigera , 9 of 14 were not found in the current genome assembly. Differences between previous and current results for the complement of MSDIN genes and cyclic peptides in the two fungi probably represents natural variation among geographically dispersed isolates of  A. phalloides  and among the members of the poorly defined  A. bisporigera  species complex. Both  A. phalloides  and  A. bisporigera  contain two prolyl oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic peptide biosynthesis as it is in  Galerina marginata .    Conclusion  The MSDIN gene family has expanded and diverged rapidly in  Amanita  section  Phalloideae . Together,  A. bisporigera  and  A. phalloides  are predicted to have the capacity to make more than 50 cyclic hexa-, hepta-, octa-, nona- and decapeptides.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3378-7) contains supplementary material, which is available to authorized users.

Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera