Psilocybe cubensis raw sequencing data

Raw dataset for genomes of Psilocybe cubensis in: https://doi.org/10.1016/j.cub.2023.10.059 Metadata are contained in the 'metadata' file and can be used to link BRIP number to sequencing number. Fungi that are edible or fermentative were domesticated through selective cultivation of their desired traits. Domestication is often associated with inbreeding or selfing, which may fix traits other than those under selection, and causes an overall decrease in heterozygosity. A hallucinogenic mushroom, Psilocybe cubensis, was domesticated from its niche in livestock dung for production of psilocybin. It has caused accidental poisonings since the 1940s in Australia, which is a population hypothesized to be introduced from an unknown center of origin. We sequenced genomes of 38 isolates from Australia and compared them with 86 genomes of commercially available cultivars to determine (1) whether P. cubensis was introduced to Australia, and (2) how domestication has impacted commercial cultivars. Our analyses of genome-wide SNPs and single-copy orthologs showed that the Australian population is naturalized, having recovered its effective population size after a bottleneck when it was introduced, and it has maintained relatively high genetic diversity based on measures of nucleotide and allelic diversity. In contrast, domesticated cultivars generally have low effective population sizes and hallmarks of selfing and clonal propagation, including low genetic diversity, low heterozygosity, high linkage disequilibrium, and low allelic diversity of mating-compatibility genes. Analyses of kinship show that most cultivars are founded from related populations. Alleles in the psilocybin gene cluster are identical across most cultivars of P. cubensis with low diversity across coding sequence; however, unique allelic diversity in Australia and some cultivars may translate to differences in biosynthesis of psilocybin and its analogs.

古巴裸盖菇（Psilocybe cubensis）基因组原始数据集，相关信息详见：https://doi.org/10.1016/j.cub.2023.10.059。元数据存储于"metadata"文件中，可用于将BRIP编号与测序编号进行关联。可食用或具备发酵特性的真菌，通常通过定向选育目标性状完成驯化。驯化过程常伴随近交或自交，这一过程可能固定除目标选育性状外的其他性状，并整体降低基因组的杂合性。致幻蘑菇古巴裸盖菇即从其原生的牲畜粪便生境中被驯化，用于裸盖菇素的规模化生产。自20世纪40年代起，澳大利亚境内的该种群便曾引发多起误食中毒事件，该种群被推测起源于一处未知的原生起源中心并被引入当地。本研究对38株澳大利亚分离株进行基因组测序，并与86株商用栽培菌株的基因组进行比对，旨在解答两个核心问题：其一，古巴裸盖菇是否为引入澳大利亚的外来物种；其二，驯化过程对商用栽培菌株产生了何种影响。基于全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与单拷贝同源基因的分析结果显示，澳大利亚种群已成功归化：该种群在引入后经历了瓶颈效应，随后恢复了有效种群规模，并基于核苷酸多样性与等位基因多样性的评估结果，维持了相对较高的遗传多样性。与之形成鲜明对比的是，商用栽培菌株通常拥有较小的有效种群规模，并具备自交与无性繁殖的典型特征：包括较低的遗传多样性、较低的杂合性、较高的连锁不平衡水平，以及交配兼容基因的低等位基因多样性。亲缘关系分析表明，绝大多数商用栽培菌株均起源于亲缘关系相近的种群。多数古巴裸盖菇栽培菌株的裸盖菇素基因簇等位基因完全一致，编码区的多样性极低；但澳大利亚种群与部分栽培菌株所特有的等位基因多样性，可能会导致裸盖菇素及其类似物的生物合成途径存在差异。