Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2024-10-28 DOI:10.1016/j.mimet.2024.107065

Kalea Gregoris, Welkin H. Pope

{"title":"Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea","authors":"Kalea Gregoris, Welkin H. Pope","doi":"10.1016/j.mimet.2024.107065","DOIUrl":null,"url":null,"abstract":"<div><div>Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.</div></div>","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0167701224001775","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}

引用次数: 0

Abstract

Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.

Abstract Image

查看原文本刊更多论文

从地衣中提取高质量元基因组 DNA

地衣是遍布温带陆地森林的复合生物，与工业空气污染有特定的物种关联。地衣样本的元基因组分析需要强大的核酸提取方法，由于地衣具有保护性皮层、多糖含量高以及内部微生物群的多样性，这一过程极具挑战性。我们的方法包括通过石榴石打珠进行物理裂解、使用十二烷基硫酸钠缓冲液进行化学裂解、苯酚：氯仿：异戊醇提取以及乙醇沉淀。该方法在来自两个不同物种的三个不同地衣样本上进行了测试，获得了适合测序和 PCR 扩增的元基因组 DNA。该方法使用普通的实验室设备和试剂，无需使用液氮，解决了从地衣中提取 DNA 的相关问题。本文介绍了一种从干燥和保存的地衣标本中获得高质量遗传物质的成本效益高且容易获得的 DNA 提取方法。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.