Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome

A complete telomere-to-telomere (T2T) genome has been a longstanding goal in the field of genomic research. By integrating high-coverage and precise long-read sequencing data using multiple assembly strategies, we present here the first T2T gap-free genome assembly of Ganoderma leucocontextum strain GL72, a Tibetan medicinal mushroom. The T2T genome, with a size of 46.69 Mb, consists 13 complete nuclear chromosomes and typical telomeric repeats (CCCTAA)n were detected at both ends of 13 chromosomes. The high mapping rate, uniform genome coverage, a complete BUSCOs of 99.7%, and base accuracy exceeding 99.999% indicate that this assembly represents the highest level of completeness and quality. Regions characterized by distinct structural attributes, including highest Hi-C interaction intensity, high repeat content, decreased gene density, low GC content, and minimal or no transcription levels across all chromosomes may represent potential centromeres. Sequence analysis revealed the first Copia centromeric retrotransposon in macro-fungi genome. Phylogenomic analysis identified that G. leucocontextum and G. tsugae diverged from the other Ganoderma species approximately 9.8-17.9 MYA. The prediction of secondary metabolic clusters confirmed the capability of this fungus to produce a substantial quantity of metabolites. This T2T gap-free genome will contribute to the genomic 'dark matter' elucidation and server as a great reference for genetics, genomics, and evolutionary studies of G. leucocontextum.

A New Species Agrocybe striatipes, also a Newly Commercially Cultivated Mushroom with Highly Nutritional and Healthy Values

The species of Agrocybe (Strophariaceae, Agaricales, Agaricomycetes) are saprophytic and widely distributed in temperate regions. In this study, a new species named Agrocybe striatipes from China is described, which has been successfully cultivated in China recently. The phenotypic characteristics examination and molecular phylogenetic analyses using multilocus data (ITS and nrLSU) both support it as a new species in the genus Agrocybe. Moreover, nutritional ingredient analysis showed that the fruiting body of A. striatipes was rich in seventeen amino acids, including eight essential amino acids, in addition to high levels of calcium (78.5 mg/kg) and vitamin D (44.1 μg/100g). The following analysis of the heavy metal contents of the fruiting bodies show that it does not contain lead, cadmium, arsenic, mercury, and other heavy metal elements. In the crude extract of the mushroom, the nutrients in the aqueous phase are amino acids and oligosaccharides, and the active substances in the ethyl acetate layer are sterols, which have a variety of pharmacological effects. In conclusion, A. striatipes is not only a new species but also has highly application values as a cultivated edible mushroom in nutrition and health.

Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Flammulina filiformis) Cultivars Identification

The enoki mushroom (Flammulina filiformis) is one of the most important and popular edible mushrooms commercially in China. However, traditional mushroom cultivar identification is challenging due to poor accuracy, heavy workloads, and low reproducibility. To overcome this challenge, we developed a method for identifying F. filiformis strains using multiple nucleotide polymorphism sequencing (MNP-seq). This involved screening 179 universal MNP markers based on whole-genome sequencing data, constructing an MNP sequence library, and performing multiplex PCR amplification and high-sequencing. We further screened 69 core MNP markers and used them to build a neighbor-joining (NJ) phylogenetic tree of 232 cultivated and wild strains. Our analysis showed that all cultivars could be accurately separated by computing genetic similarity values and that the cultivars could be separated into 22 distinct evolutionary pedigrees. The specific value of genetic similarity can be used as the standard to distinguish F. filiformis cultivars, however, it needs to be comprehensively defined by the additional phenotype and biological characteristics of those strains in the future work.