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

文献类型： 外文期刊

作者： Gao, Qi 1 ; Yan, Dong 1 ; Song, Shuang 1 ; Fan, Yangyang 1 ; Wang, Shouxian 1 ; Liu, Yu 1 ; Huang, Yu 1 ; Rong, Chengbo 1 ; Guo, Yuan 1 ; Zhao, Shuang 1 ; Qin, Wentao 1 ; Xu, Jianping 5 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Inst Plant Protect, Beijing Engn Res Ctr Edible Mushroom, 9 Shuguang Garden Zhonglu, Beijing 100097, Peoples R China

2.Peking Univ, Sch Adv Agr Sci, Peking Tsinghua Ctr Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China

3.Baise Univ, Coll Agr & Food Engn, 21 Zhongshan Second St, Baise 533000, Peoples R China

4.Beijing Acad Agr & Forestry Sci, Inst Agri Food Proc & Nutr, Beijing 100097, Peoples R China

5.McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada

关键词： Lentinula edodes; de novo; comparative genomics; hybridization; dikaryon; dedikaryotization; monokaryons; gene enrichment; mating-type loci

期刊名称：JOURNAL OF FUNGI （ 影响因子：5.724； 五年影响因子：6.413 ）

ISSN：

年卷期： 2022 年 8 卷 2 期

页码：

收录情况： SCI

摘要： 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.

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