Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis

Abstract

Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the “queen of the mushroom” for its attractive appearance. D. 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 lack of genomic information, research on the bioactive substance, cross breeding, lignocellulose degradation, and molecular biology were limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single molecule real time (SMRT) 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 Mb 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 non-coding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding gene were predicted, among which there were 8,830 (90.79%) genes were predicted using homology or RNAseq-predicted. BUSCO results further revealed that there were 80.34% complete single-copy fungal orthologs. A total of 360 genes were annotated as belonging to Carbohydrate-active enzymes (CAZymes) family in this study. 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.

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

“…Our study is also among the first to employ Hi-C sequencing in fungal surveys, resulting in high-quality contact maps and improved genome assembly. This approach has only recently been applied to edible and medicinal mushrooms [64]. The substantial improvement in assembly quality suggests that, following the spirit of the Earth Biogenome Project [65], outlining the genomic diversity of fungi can be efficiently achieved using Hi-C sequencing, following a methodological platform such as DNA Zoo (http://www.dnazoo.org, (accessed on 10 November 2022)), for the cost-effective generation of high-quality fungal genomes.…”