Genomic tools for Psilocybe cubensis propagation
Psilocybe cubensis is a fungus that synthesizes therapeutic quantities of psilocybin, psilocin, and other active tryptamines. Understanding the genetic variation in this synthesis pathway can shed light on variants responsible for specific chemotypes. To better understand this diversity, we first built a reference grade genome of Psilocybe cubensis. Using Pacific Biosciences HiFi sequencing and Phase Genomics Proximity ligation assay (HiC), we constructed a chromosome scale, annotated reference genome for Psilocybe cubensis. The genome now contains 13 chromosomes, 46Mb with an N50 contig lengths of 3.6Mb. Several chromosomes are tip to tip chromosomes with visible telomeres on each end. Using this reference genome, we have sequenced and mapped an additional 81 Psilocybe genomes to catalog the genetic diversity and microbial contaminants frequently found in this genus. These data have been used to design quantitative polymerase chain reaction (qPCR) assays for Psilocybe cubensis identification from spores or tissue. Multiplex qPCR assays have been designed for simultaneous quantification of E. coli and Salmonella species contamination concurrent with Psilocybe cubensis species identification. Included in the genome annotations are two mating type genes and four pheromone receptors responsible for mating type classification. These tools can assist in directed breeding of the species, contaminant identification and P. cubensis species verification.