Yan Xu , Xumeng Huo , Xinyue Chen , Zeyang Wang , Mingliang Zhou , Jie Zhu , Rui Yan , Yanpeng Cai
{"title":"比较不同 eDNA 引物在鱼类监测中的性能差异","authors":"Yan Xu , Xumeng Huo , Xinyue Chen , Zeyang Wang , Mingliang Zhou , Jie Zhu , Rui Yan , Yanpeng Cai","doi":"10.1016/j.wsee.2024.08.003","DOIUrl":null,"url":null,"abstract":"<div><p>Environmental DNA technology develops rapidly in the field of biodiversity detection. Selecting appropriate primers may be one of the key questions. However, there is currently a lack of systematic studies on differences in primer detection efficiencies. This research investigates the efficiency of six universal primers (12S, 16S, 18S, MiFish, Cytb, and COI) in detecting fish species across diverse aquatic ecosystems using an environmental DNA approach. The research spans five study areas, representing marine, river, wetland, lake, and reservoir ecosystems. Illumina MiSeq sequencing and bioinformatics tools were employed for primer performance evaluation. Results indicate that MiFish consistently outperforms other primers, detecting the highest number of fish species across all ecosystems and exhibiting superior taxonomic coverage. Furthermore, marine ecosystems consistently show higher detection numbers across all primers. The absence of commonly identified species detected by all primers emphasizes the necessity of using multiple primers for a comprehensive assessment. This study provides valuable insights into the strengths and limitations of universal primers, highlighting the importance of primer selection for accurate eDNA-based fish monitoring. The findings contribute to the scientific basis for the comprehensive management of aquatic ecosystems, assisting researchers and ecosystem managers in screening suitable fish universal primers for eDNA methods. The study also calls for further research into factors influencing primer performance and encourages the refinement of primers to enhance biodiversity monitoring precision in various ecosystems.</p></div>","PeriodicalId":101280,"journal":{"name":"Watershed Ecology and the Environment","volume":"6 ","pages":"Pages 165-175"},"PeriodicalIF":0.0000,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2589471424000135/pdfft?md5=a8fbb323cf57517c6d1b8d4998599e24&pid=1-s2.0-S2589471424000135-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Comparing the performance variability of different eDNA primers in fish monitoring\",\"authors\":\"Yan Xu , Xumeng Huo , Xinyue Chen , Zeyang Wang , Mingliang Zhou , Jie Zhu , Rui Yan , Yanpeng Cai\",\"doi\":\"10.1016/j.wsee.2024.08.003\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Environmental DNA technology develops rapidly in the field of biodiversity detection. Selecting appropriate primers may be one of the key questions. However, there is currently a lack of systematic studies on differences in primer detection efficiencies. This research investigates the efficiency of six universal primers (12S, 16S, 18S, MiFish, Cytb, and COI) in detecting fish species across diverse aquatic ecosystems using an environmental DNA approach. The research spans five study areas, representing marine, river, wetland, lake, and reservoir ecosystems. Illumina MiSeq sequencing and bioinformatics tools were employed for primer performance evaluation. Results indicate that MiFish consistently outperforms other primers, detecting the highest number of fish species across all ecosystems and exhibiting superior taxonomic coverage. Furthermore, marine ecosystems consistently show higher detection numbers across all primers. The absence of commonly identified species detected by all primers emphasizes the necessity of using multiple primers for a comprehensive assessment. This study provides valuable insights into the strengths and limitations of universal primers, highlighting the importance of primer selection for accurate eDNA-based fish monitoring. The findings contribute to the scientific basis for the comprehensive management of aquatic ecosystems, assisting researchers and ecosystem managers in screening suitable fish universal primers for eDNA methods. The study also calls for further research into factors influencing primer performance and encourages the refinement of primers to enhance biodiversity monitoring precision in various ecosystems.</p></div>\",\"PeriodicalId\":101280,\"journal\":{\"name\":\"Watershed Ecology and the Environment\",\"volume\":\"6 \",\"pages\":\"Pages 165-175\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2589471424000135/pdfft?md5=a8fbb323cf57517c6d1b8d4998599e24&pid=1-s2.0-S2589471424000135-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Watershed Ecology and the Environment\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2589471424000135\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Watershed Ecology and the Environment","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2589471424000135","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
环境 DNA 技术在生物多样性检测领域发展迅速。选择合适的引物可能是关键问题之一。然而,目前缺乏对引物检测效率差异的系统研究。本研究采用环境 DNA 方法,调查了六种通用引物(12S、16S、18S、MiFish、Cytb 和 COI)在不同水生生态系统中检测鱼类物种的效率。该研究横跨五个研究区域,分别代表海洋、河流、湿地、湖泊和水库生态系统。采用 Illumina MiSeq 测序和生物信息学工具进行引物性能评估。结果表明,MiFish 的性能始终优于其他引物,在所有生态系统中检测到的鱼类物种数量最多,分类覆盖率也更高。此外,海洋生态系统在所有引物中都显示出较高的检测数量。所有引物都没有检测到共同识别的物种,这强调了使用多种引物进行综合评估的必要性。这项研究对通用引物的优势和局限性提供了宝贵的见解,强调了选择引物对基于 eDNA 的鱼类精确监测的重要性。研究结果为水生生态系统的综合管理提供了科学依据,有助于研究人员和生态系统管理人员为 eDNA 方法筛选合适的鱼类通用引物。该研究还呼吁进一步研究影响引物性能的因素,并鼓励改进引物,以提高各种生态系统中生物多样性监测的精确度。
Comparing the performance variability of different eDNA primers in fish monitoring
Environmental DNA technology develops rapidly in the field of biodiversity detection. Selecting appropriate primers may be one of the key questions. However, there is currently a lack of systematic studies on differences in primer detection efficiencies. This research investigates the efficiency of six universal primers (12S, 16S, 18S, MiFish, Cytb, and COI) in detecting fish species across diverse aquatic ecosystems using an environmental DNA approach. The research spans five study areas, representing marine, river, wetland, lake, and reservoir ecosystems. Illumina MiSeq sequencing and bioinformatics tools were employed for primer performance evaluation. Results indicate that MiFish consistently outperforms other primers, detecting the highest number of fish species across all ecosystems and exhibiting superior taxonomic coverage. Furthermore, marine ecosystems consistently show higher detection numbers across all primers. The absence of commonly identified species detected by all primers emphasizes the necessity of using multiple primers for a comprehensive assessment. This study provides valuable insights into the strengths and limitations of universal primers, highlighting the importance of primer selection for accurate eDNA-based fish monitoring. The findings contribute to the scientific basis for the comprehensive management of aquatic ecosystems, assisting researchers and ecosystem managers in screening suitable fish universal primers for eDNA methods. The study also calls for further research into factors influencing primer performance and encourages the refinement of primers to enhance biodiversity monitoring precision in various ecosystems.