An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences Pub Date : 2023-04-27 DOI:10.1002/aps3.11518

Maryam Hadi, Elizabeth A. Stacy

{"title":"An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex","authors":"Maryam Hadi, Elizabeth A. Stacy","doi":"10.1002/aps3.11518","DOIUrl":null,"url":null,"abstract":"<div>\n \n \n <section>\n \n <h3> Premise</h3>\n \n <p>The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse <i>Metrosideros</i> taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites.</p>\n </section>\n \n <section>\n \n <h3> Methods and Results</h3>\n \n <p>We tested popular RNA isolation kits and protocols that were effective on other recalcitrant trees, including a broad range of optimization and purification steps. We optimized a protocol involving two silica-membrane column-based kits that yielded high-quantity RNA with an RNA integrity number >7 and without DNA contamination. All RNA samples were used successfully in a follow-on RNA-Seq experiment.</p>\n </section>\n \n <section>\n \n <h3> Conclusions</h3>\n \n <p>We present an optimized high-throughput RNA extraction protocol that yielded high-quality and high-quantity RNA from three contrasting leaf phenotypes within a hyperdiverse woody species complex.</p>\n </section>\n </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 3","pages":""},"PeriodicalIF":2.7000,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11518","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Applications in Plant Sciences","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/aps3.11518","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PLANT SCIENCES","Score":null,"Total":0}

引用次数: 2

Abstract

Premise

The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse Metrosideros taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites.

Methods and Results

We tested popular RNA isolation kits and protocols that were effective on other recalcitrant trees, including a broad range of optimization and purification steps. We optimized a protocol involving two silica-membrane column-based kits that yielded high-quantity RNA with an RNA integrity number >7 and without DNA contamination. All RNA samples were used successfully in a follow-on RNA-Seq experiment.

Conclusions

We present an optimized high-throughput RNA extraction protocol that yielded high-quality and high-quantity RNA from three contrasting leaf phenotypes within a hyperdiverse woody species complex.

Abstract Image

查看原文本刊更多论文

一种优化的高变树种复合体夏威夷Metrosideros不同叶片RNA提取方法

前提条件由于多酚和多糖对下游过程的干扰，从树木中分离RNA具有挑战性。此外，许多RNA提取方案耗时且涉及危险化学品。为了解决这些问题，我们旨在开发一种安全的方案，从不同的Metrosideros分类群中提取高质量的RNA，这些分类群代表了广泛的叶片韧性、青春期和次生代谢产物。方法和结果我们测试了流行的RNA分离试剂盒和方案，这些试剂盒和协议对其他顽抗树有效，包括广泛的优化和纯化步骤。我们优化了涉及两个基于二氧化硅膜柱的试剂盒的方案，其产生具有RNA完整性数>；7并且没有DNA污染。所有的RNA样品都成功地用于后续的RNA-Seq实验。结论我们提出了一种优化的高通量RNA提取方案，该方案从高度多样化的木本物种复合体中的三种不同的叶片表型中产生高质量和高数量的RNA。

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

Applications in Plant Sciences PLANT SCIENCES-

CiteScore

7.30

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America, originating in 2009 as the American Journal of Botany''s online-only section, AJB Primer Notes & Protocols in the Plant Sciences. APPS publishes the following types of articles: (1) Protocol Notes describe new methods and technological advancements; (2) Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes; (3) Software Notes detail new software applications; (4) Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study; (5) Review Articles evaluate available techniques, methods, or protocols; (6) Primer Notes report novel genetic markers with evidence of wide applicability.