Nearly telomere-to-telomere genome assembly of the L. edodes diploid genome

IF 2.4 3区生物学 Q3 GENETICS & HEREDITY

Fungal Genetics and Biology Pub Date : 2025-05-23 DOI:10.1016/j.fgb.2025.104005

Kazutoshi Yoshitake , Kenta Shirasawa , Kenji K. Kojima , Shuichi Asakawa , Norio Tanaka , Hiroyuki Kurokochi

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引用次数: 0

Abstract

Lentinula edodes (shiitake mushroom) possesses substantial nutritional and medicinal value. Even though the genomes of several strains have been reported, some essential observations, including the exact chromosome number, still need validation. This study reports a near-telomere-to-telomere assembly of the complete diploid genome of L. edodes strain XR1, a commercially important Japanese strain. We employed the PacBio HiFi long-read sequencing technology combined with single-cell genotyping data and manual curation. The assembled diploid genome comprised 20 chromosomes (10 per haplotype), and significant inter-haplotype variation was observed. Additionally, we identified a novel Penelope-like retrotransposon—Coprina-1_LeEd—specifically localized to the telomeres. This study marks the first report of telomere elongation by the transposition of Coprina. Our findings provide a high-resolution genome resource for L. edodes, consequently elucidating its evolution, genomic structure, and breeding potential. Furthermore, this study establishes a foundation for further research on edible mushroom genetics and biotechnology.

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黑桫椤二倍体基因组的近端粒到端粒基因组组装。

香菇（香菇）具有丰富的营养和药用价值。尽管已经报道了几种菌株的基因组，但一些重要的观察结果，包括确切的染色体数目，仍然需要验证。本研究报道了L. edodes菌株XR1完整二倍体基因组的近端粒到端粒组装，这是一种具有重要商业价值的日本菌株。我们采用PacBio HiFi长读测序技术，结合单细胞基因分型数据和人工管理。组装后的二倍体基因组包含20条染色体（每单倍型10条），单倍型间存在显著差异。此外，我们发现了一种新的类似penelope的反转录转座子coprina - 1_leed -特异性定位于端粒。本研究首次报道了Coprina转位引起的端粒延长。我们的发现提供了高分辨率的L. edodes基因组资源，从而阐明了其进化，基因组结构和育种潜力。为进一步开展食用菌遗传与生物技术研究奠定了基础。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Fungal Genetics and Biology 生物-遗传学

CiteScore

6.20

自引率

3.30%

发文量

审稿时长

85 days

期刊介绍： Fungal Genetics and Biology, formerly known as Experimental Mycology, publishes experimental investigations of fungi and their traditional allies that relate structure and function to growth, reproduction, morphogenesis, and differentiation. This journal especially welcomes studies of gene organization and expression and of developmental processes at the cellular, subcellular, and molecular levels. The journal also includes suitable experimental inquiries into fungal cytology, biochemistry, physiology, genetics, and phylogeny. Fungal Genetics and Biology publishes basic research conducted by mycologists, cell biologists, biochemists, geneticists, and molecular biologists. Research Areas include: • Biochemistry • Cytology • Developmental biology • Evolutionary biology • Genetics • Molecular biology • Phylogeny • Physiology.