Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes

Abstract

Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes.

Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication

“…The difference in the number of core genes in different genomes may be due to the diverse quality of genome assembly, which may result in discrepancies in the types and numbers of genes predicted. Like L. edodes [ 1 ], the core genes of A. heimuer covered the genetic programs of basic life processes such as cell growth and fruiting body development. In the future, larger-scale research into the A. heimuer pan-genome is necessary to discover the key gene families associated with agronomic traits.…”

“…Due to genetic variation between individuals of the same species, the use of a single reference genome implies the missing of a large amount of important genetic information. In addition, basidiomycetes are dikaryotic and have two sets of diverse genomes [ 1 ]. At present, only one set of the monokaryotic genome sequence is usually used to represent all of the genetic information of the species, causing further loss of genetic information.…”

“…Evidence of species pan-genome viability has also been confirmed in fungi [ 11 , 12 , 13 , 14 , 15 ]. However, to date, in the pan-genome study of macrofungi, there is only a single report concerning core gene families in Lentinula edodes [ 1 ].…”

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

“…The authors found differences in genome size, organization and genetic content [96]. Nevertheless, haplotype-resolved genomes of Lentinula edodes (Agaricales, Basidiomycota), achieved by protoplast dedikaryotization, next-generation sequencing (NGS) and optical mapping, showed slight differences in genome size, but strong differences in the content and genetic organization of each nucleus [25]. The content and genetic organization discordance of the two nuclei in L. trichodermophora strains may explain the assembly fragmentation and size differences.…”

Correction: Gao et al. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J. Fungi 2022, 8, 167

“…In the original article [ 1 ], the information regarding the SP30 unique gene was not correct. The authors wish to make the following corrections to this paper, which was published in the Journal of Fungi .…”