Establishing an Interactive Sequence Database for Shiitake Cultivar Identification.

IF 3.5 4区 生物学 Q2 MICROBIOLOGY Journal of Basic Microbiology Pub Date : 2024-11-05 DOI:10.1002/jobm.202400452
Jie-Hao Ou, Han-Yun Li, Yun-Shen Lu, Chi-Yu Chen, Yu-Hsuan Fan, Guan Jie Phang, Guan-Ying Huang, Sung-Yuan Hsieh, Yin-Tse Huang
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引用次数: 0

Abstract

Shiitake mushrooms (Lentinula edodes) hold significant cultural and economic value, particularly in Asia where they are extensively cultivated. The diversification of shiitake cultivars, driven by the need to adapt to various climatic conditions and cultivation methods, has resulted in over 200 distinct cultivars. Reliable identification of these cultivars is crucial for breeding, intellectual property protection, and effective genetic resource management. Traditional morphological methods are inadequate due to their subjectivity and labor-intensive nature. This study leverages nanopore high-throughput sequencing to comprehensively analyze the rDNA regions (SSU, ITS, LSU, IGS) of 41 shiitake strains from Taiwan's Bioresource Collection and Research Center (BCRC), comprising 5 wild strains, 33 commercial strains, and 3 wild-commercial hybrids. Our results identified the IGS1 region as the most variable and suitable for cultivar differentiation. Consequently, we developed an interactive online database (https://github.com/Raingel/ShiitakeIGS1) that integrates 317 IGS1 sequences from Taiwan, Japan, and China. This platform allows users to upload their IGS1 sequences and identify similar cultivars through a user-friendly interface, enhancing the precision and efficiency of shiitake cultivar identification.

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建立香菇栽培品种鉴定互动序列数据库
香菇(Lentinula edodes)具有重要的文化和经济价值,尤其是在广泛种植香菇的亚洲。由于需要适应各种气候条件和栽培方法,香菇栽培品种不断多样化,目前已有 200 多个不同的栽培品种。这些栽培品种的可靠鉴定对于育种、知识产权保护和有效的遗传资源管理至关重要。传统的形态学方法因其主观性和劳动密集型而存在不足。本研究利用纳米孔高通量测序技术,全面分析了台湾生物资源收集与研究中心(BCRC)41个香菇菌株的rDNA区域(SSU、ITS、LSU、IGS),包括5个野生菌株、33个商业菌株和3个野生-商业杂交种。我们的研究结果表明,IGS1 区域的变化最大,适合用于栽培品种的区分。因此,我们开发了一个交互式在线数据库(https://github.com/Raingel/ShiitakeIGS1),整合了来自台湾、日本和中国的 317 个 IGS1 序列。该平台允许用户上传其 IGS1 序列,并通过友好的用户界面识别相似的栽培品种,从而提高香菇栽培品种鉴定的精确度和效率。
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来源期刊
Journal of Basic Microbiology
Journal of Basic Microbiology 生物-微生物学
CiteScore
6.10
自引率
0.00%
发文量
134
审稿时长
1.8 months
期刊介绍: The Journal of Basic Microbiology (JBM) publishes primary research papers on both procaryotic and eucaryotic microorganisms, including bacteria, archaea, fungi, algae, protozoans, phages, viruses, viroids and prions. Papers published deal with: microbial interactions (pathogenic, mutualistic, environmental), ecology, physiology, genetics and cell biology/development, new methodologies, i.e., new imaging technologies (e.g. video-fluorescence microscopy, modern TEM applications) novel molecular biology methods (e.g. PCR-based gene targeting or cassettes for cloning of GFP constructs).
期刊最新文献
Establishing an Interactive Sequence Database for Shiitake Cultivar Identification. Cover: Journal of Basic Microbiology. 11/2024 Issue Information: Journal of Basic Microbiology. 11/2024 Role of Orphan ParA Proteins in Replication and Cell Division in Rhodococcus erythropolis PR4. Biocatalytic Potential of Pseudomonas Species in the Degradation of Polycyclic Aromatic Hydrocarbons.
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