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

Lu Ma; Chi Yang; Donglai Xiao; Xiaoyu Liu; Xiaoling Jiang; Hui Lin; Zhenghe Ying; Yanquan Lin

doi:10.1093/g3journal/jkad102

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

G3 (Bethesda). 2023 Aug 9;13(8):jkad102. doi: 10.1093/g3journal/jkad102.

Authors

Lu Ma^{1

2}, Chi Yang^{1

2}, Donglai Xiao^{1

2}, Xiaoyu Liu^{1

2}, Xiaoling Jiang^{1

2}, Hui Lin^{1

2}, Zhenghe Ying^{1

2}, Yanquan Lin^{1

2}

Affiliations

¹ Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China.
² National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China.

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. 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.

Keywords: Dictyophora rubrovolvata; CAZymes; functional annotation; lignocellulose degradation; whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes*
Molecular Sequence Annotation
Phylogeny
Plant Breeding*
Sequence Analysis, DNA

Supplementary concepts

Dictyophora rubrovolvata