不同 Lentinula edodes (Berk.) Pegler 菌株之间的转录变异和 RNA 多态性。

IF 3.3 2区农林科学 Q1 AGRICULTURE, MULTIDISCIPLINARY Journal of the Science of Food and Agriculture Pub Date : 2024-10-18 DOI:10.1002/jsfa.13960

Sujata Makkar, Rama Shankar, Ajay Singh, Sudheer Kumar Annepu, Kiran Nehra

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引用次数: 0

摘要

背景：冬菇是一种具有重要商业价值的蘑菇，因其营养和治疗价值而闻名。然而，人们对不同小扁豆菌株具有不同营养和生理特性的分子机制还不甚了解。本研究重点研究了三种具有不同营养和生产力特征的扁平苔藓菌株（DMRO-356、DMRO-623 和 DMRO-388s）。采用 Illumina 测序技术进行全转录组分析，对总信使核糖核酸（mRNA）进行一式两份的 100 碱基对成对测序，每个菌株可获得 2,800-4,800 万个测序读数。经过严格的数据过滤，99%以上的高质量读数被保留下来，95%以上的读数与扁豆基因组进行了比对：差异基因表达分析确定了 DMRO-356 和 DMRO-623 之间有 2210 个差异表达基因，DMRO-356 和 DMRO-388s 之间有 862 个差异表达基因，DMRO-623 和 DMRO-388s 之间有 2212 个差异表达基因。在菌株之间发现了显著的遗传变异，包括 DMRO-356 与 DMRO-623 之间的 7753 个单核苷酸多态性（SNPs），以及 DMRO-356 与 DMRO-388s 之间的 4080 个 SNPs。此外，在 DMRO-356/DMRO-623 中发现了 349 个插入/缺失（InDels），在 DMRO-356/DMRO-388s 中发现了 218 个插入/缺失（InDels）。对改变氨基酸组成的非同义 SNP 进行了分析，结果显示极性氨基酸优于带电氨基酸：结论：这些差异表达基因与各种营养和发育过程有关，凸显了基因变异在形成氨基酸组成和潜在影响蛋白质功能方面的重要性。这项研究首次全面探讨了可供栽培的扁豆菌株之间的转录差异，为提高蘑菇质量和产量提供了宝贵的见解。© 2024 化学工业协会。

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Transcriptional variation and RNA polymorphism among different Lentinula edodes (Berk.) Pegler strains.

Background: Lentinula edodes is a commercially important mushroom known for its nutritional and therapeutic values. However, the molecular mechanisms underlying the distinct nutritional and physiological attributes of various L. edodes strains are not well understood. This study focused on three Lentinula strains (DMRO-356, DMRO-623, and DMRO-388s) with different nutritional and productivity profiles. Illumina sequencing was used to perform a whole-transcriptome analysis, conducting 100-base pair paired-end sequencing of total messenger RNA (mRNA) in duplicate, resulting in 28-48 million sequencing reads per strain. After rigorous data filtering, over 99% of high-quality reads were retained, and more than 95% were aligned to the Lentinula genome.

Results: Differential gene expression analyses identified 2210 differentially expressed genes between DMRO-356 and DMRO-623, 862 between DMRO-356 and DMRO-388s, and 2212 between DMRO-623 and DMRO-388s. Significant genetic variations were found among the strains, including 7753 single nucleotide polymorphisms (SNPs) in DMRO-356 versus DMRO-623 and 4080 SNPs in DMRO-356 versus DMRO-388s. Additionally, 349 insertions/deletions (InDels) were found in DMRO-356/DMRO-623 and 218 in DMRO-356/DMRO-388 s. Non-synonymous SNPs, which alter amino acid compositions, were analyzed, showing a preference for polar over charged amino acids.

Conclusion: These differentially expressed genes were associated with various nutritional and developmental processes, highlighting the importance of genetic variations in shaping amino acid composition and potentially affecting protein function. This study is the first comprehensive exploration of transcriptional differences among Lentinula strains available for its cultivation, providing valuable insights to enhance mushroom quality and productivity. © 2024 Society of Chemical Industry.

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来源期刊

Journal of the Science of Food and Agriculture 工程技术-农业综合

CiteScore

8.10

自引率

4.90%

发文量

634

审稿时长

3.1 months

期刊介绍： The Journal of the Science of Food and Agriculture publishes peer-reviewed original research, reviews, mini-reviews, perspectives and spotlights in these areas, with particular emphasis on interdisciplinary studies at the agriculture/ food interface. Published for SCI by John Wiley & Sons Ltd. SCI (Society of Chemical Industry) is a unique international forum where science meets business on independent, impartial ground. Anyone can join and current Members include consumers, business people, environmentalists, industrialists, farmers, and researchers. The Society offers a chance to share information between sectors as diverse as food and agriculture, pharmaceuticals, biotechnology, materials, chemicals, environmental science and safety. As well as organising educational events, SCI awards a number of prestigious honours and scholarships each year, publishes peer-reviewed journals, and provides Members with news from their sectors in the respected magazine, Chemistry & Industry . Originally established in London in 1881 and in New York in 1894, SCI is a registered charity with Members in over 70 countries.