{"title":"使用 DESS 保存解决方案从标本和环境样本中无损提取 DNA,用于 DNA 条形码分析","authors":"Eri Ogiso-Tanaka, Minako Abe Ito, Daisuke Shimada","doi":"10.1101/2024.08.09.607403","DOIUrl":null,"url":null,"abstract":"DESS is a widely used storage solution for the preservation of DNA from biological tissue samples. DESS comprises 20% dimethyl sulfoxide, 250 mM ethylenediaminetetraacetic acid, and saturated sodium chloride, and its efficacy has been confirmed in various taxa and tissues. DESS enables the stable, long-term preservation of both sample morphology and DNA. However, to access the DNA, excising a portion of the sample was necessary. Although DNA is a valuable source of information for species identification, DNA extraction can result in the loss of an entire sample or segment, especially in small-sized organisms, thereby compromising specimen value. Therefore, establishing non-destructive DNA extraction techniques is imperative. Thus, this paper presents a protocol for conducting non-destructive DNA extraction and DNA barcoding using a portion of the DESS supernatant obtained from a nematode specimen. This method was successfully employed for DNA barcoding of nematodes that were stored in DESS at room temperature (-10~35˚C) for ten years. Moreover, the method can be potentially applied in the preservation and non-destructive extraction of DNA from specimens of various species. Following sample collection, a bulk environmental sample from sediment and seagrass is immediately immersed in DESS in the field. Subsequently, DNA is extracted from the supernatant solution, allowing non-destructive DNA barcoding. Overall, this paper presents comprehensive protocols for DNA extraction from DESS supernatants and demonstrates their practical application using meiofauna (small animals) and diatoms as examples.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"6 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Non-destructive DNA extraction from specimens and environmental samples using DESS preservation solution for DNA barcoding\",\"authors\":\"Eri Ogiso-Tanaka, Minako Abe Ito, Daisuke Shimada\",\"doi\":\"10.1101/2024.08.09.607403\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"DESS is a widely used storage solution for the preservation of DNA from biological tissue samples. DESS comprises 20% dimethyl sulfoxide, 250 mM ethylenediaminetetraacetic acid, and saturated sodium chloride, and its efficacy has been confirmed in various taxa and tissues. DESS enables the stable, long-term preservation of both sample morphology and DNA. However, to access the DNA, excising a portion of the sample was necessary. Although DNA is a valuable source of information for species identification, DNA extraction can result in the loss of an entire sample or segment, especially in small-sized organisms, thereby compromising specimen value. Therefore, establishing non-destructive DNA extraction techniques is imperative. Thus, this paper presents a protocol for conducting non-destructive DNA extraction and DNA barcoding using a portion of the DESS supernatant obtained from a nematode specimen. This method was successfully employed for DNA barcoding of nematodes that were stored in DESS at room temperature (-10~35˚C) for ten years. Moreover, the method can be potentially applied in the preservation and non-destructive extraction of DNA from specimens of various species. Following sample collection, a bulk environmental sample from sediment and seagrass is immediately immersed in DESS in the field. Subsequently, DNA is extracted from the supernatant solution, allowing non-destructive DNA barcoding. Overall, this paper presents comprehensive protocols for DNA extraction from DESS supernatants and demonstrates their practical application using meiofauna (small animals) and diatoms as examples.\",\"PeriodicalId\":501246,\"journal\":{\"name\":\"bioRxiv - Genetics\",\"volume\":\"6 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-08-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv - Genetics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2024.08.09.607403\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv - Genetics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.08.09.607403","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
DESS 是一种广泛使用的生物组织样本 DNA 保存液。DESS 由 20% 二甲基亚砜、250 mM 乙二胺四乙酸和饱和氯化钠组成,其功效已在不同类群和组织中得到证实。DESS 可以长期稳定地保存样本形态和 DNA。不过,要获取 DNA,必须切除部分样本。虽然 DNA 是物种鉴定的宝贵信息来源,但 DNA 提取可能会导致整个样本或样本片段的损失,尤其是在小型生物体中,从而影响标本的价值。因此,建立非破坏性的 DNA 提取技术势在必行。因此,本文介绍了一种利用从线虫标本中获得的部分 DESS 上清液进行非破坏性 DNA 提取和 DNA 条形码的方法。该方法被成功地用于对在室温(-10~35˚C)下储存在 DESS 中的线虫进行 DNA 条形编码。此外,该方法还可用于保存和无损提取不同物种标本中的 DNA。样本采集完成后,在野外立即将沉积物和海草的大量环境样本浸入 DESS 中。随后,从上清液中提取 DNA,从而实现非破坏性 DNA 条形编码。总之,本文介绍了从 DESS 上清液中提取 DNA 的综合方案,并以小型动物和硅藻为例展示了其实际应用。
Non-destructive DNA extraction from specimens and environmental samples using DESS preservation solution for DNA barcoding
DESS is a widely used storage solution for the preservation of DNA from biological tissue samples. DESS comprises 20% dimethyl sulfoxide, 250 mM ethylenediaminetetraacetic acid, and saturated sodium chloride, and its efficacy has been confirmed in various taxa and tissues. DESS enables the stable, long-term preservation of both sample morphology and DNA. However, to access the DNA, excising a portion of the sample was necessary. Although DNA is a valuable source of information for species identification, DNA extraction can result in the loss of an entire sample or segment, especially in small-sized organisms, thereby compromising specimen value. Therefore, establishing non-destructive DNA extraction techniques is imperative. Thus, this paper presents a protocol for conducting non-destructive DNA extraction and DNA barcoding using a portion of the DESS supernatant obtained from a nematode specimen. This method was successfully employed for DNA barcoding of nematodes that were stored in DESS at room temperature (-10~35˚C) for ten years. Moreover, the method can be potentially applied in the preservation and non-destructive extraction of DNA from specimens of various species. Following sample collection, a bulk environmental sample from sediment and seagrass is immediately immersed in DESS in the field. Subsequently, DNA is extracted from the supernatant solution, allowing non-destructive DNA barcoding. Overall, this paper presents comprehensive protocols for DNA extraction from DESS supernatants and demonstrates their practical application using meiofauna (small animals) and diatoms as examples.