Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China.
National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China.
G3 (Bethesda). 2023 Aug 9;13(8). doi: 10.1093/g3journal/jkad102.
Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the "queen of the mushroom" for its attractive appearance. Dictyophora rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition, and artificial cultivation. Due to a lack of genomic information, research on bioactive substances, cross breeding, lignocellulose degradation, and molecular biology is limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single-molecule real-time-sequencing technique and high-throughput chromosome conformation capture (Hi-C) technologies. A total of 1.83 Gb circular consensus sequencing reads representing ∼983.34 coverage of the D. rubrovolvata genome were generated. The final genome was assembled into 136 contigs with a total length of 32.89 Mb. The scaffold and contig N50 length were 2.71 and 2.48 Mb, respectively. After chromosome-level scaffolding, 11 chromosomes with a total length of 28.24 Mb were constructed. Genome annotation further revealed that 9.86% of the genome was composed of repetitive sequences, and a total of 508 noncoding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding genes were predicted, among which 8,830 (90.79%) genes were predicted using homology or RNA-seq. Benchmarking Universal Single-Copy Orthologs results further revealed that there were 80.34% complete single-copy fungal orthologs. In this study, a total of 360 genes were annotated as belonging to the carbohydrate-active enzymes family. Further analysis also predicted 425 cytochromes P450 genes, which can be classified into 41 families. This highly accurate, chromosome-level reference genome of D. rubrovolvata will provide essential genomic information for understanding the molecular mechanism in its fruiting body formation during morphological development and facilitate the exploitation of medicinal compounds produced by this mushroom.
皱柄白马鞍菌，一种具有营养和药用价值的珍稀食用蘑菇，因其外观诱人而被誉为“蘑菇皇后”。近年来，皱柄白马鞍菌在中国得到了广泛的人工栽培，许多研究人员专注于其营养、培养条件、人工栽培等方面的研究。由于缺乏基因组信息，其生物活性物质、杂交育种、木质纤维素降解和分子生物学等方面的研究受到限制。在本研究中，我们使用 PacBio 单分子实时测序技术和高通量染色体构象捕获（Hi-C）技术，报道了皱柄白马鞍菌的染色体水平参考基因组。共生成了 1.83 Gb 的圆形一致测序reads，代表皱柄白马鞍菌基因组约 983.34 的覆盖率。最终基因组组装成 136 个contigs，总长度为 32.89 Mb。支架和 contig N50 长度分别为 2.71 和 2.48 Mb。染色体水平支架后，构建了 11 条总长 28.24 Mb 的染色体。基因组注释进一步表明，基因组的 9.86%由重复序列组成，共注释了 508 个非编码 RNA（rRNA：329，tRNA：150，ncRNA：29）。此外，预测了 9725 个蛋白质编码基因，其中 8830 个（90.79%）基因使用同源性或 RNA-seq 进行预测。基准通用单拷贝直系同源物的结果进一步表明，有 80.34%的完整单拷贝真菌直系同源物。在本研究中，共注释了 360 个属于碳水化合物活性酶家族的基因。进一步分析还预测了 425 个细胞色素 P450 基因，可分为 41 个家族。皱柄白马鞍菌的全基因组图谱为理解其在形态发育过程中果实形成的分子机制提供了重要的基因组信息，并有助于开发该蘑菇产生的药用化合物。
