{"title":"包括数据库外群减少假阳性真菌元条形码分类分配。","authors":"Clayton Rawson, Geoffrey Zahn","doi":"10.1080/00275514.2023.2206931","DOIUrl":null,"url":null,"abstract":"<p><p>Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as <i>Fungus</i> sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.</p>","PeriodicalId":18779,"journal":{"name":"Mycologia","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments.\",\"authors\":\"Clayton Rawson, Geoffrey Zahn\",\"doi\":\"10.1080/00275514.2023.2206931\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as <i>Fungus</i> sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.</p>\",\"PeriodicalId\":18779,\"journal\":{\"name\":\"Mycologia\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2023-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Mycologia\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1080/00275514.2023.2206931\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MYCOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Mycologia","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1080/00275514.2023.2206931","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MYCOLOGY","Score":null,"Total":0}
Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments.
Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as Fungus sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.
期刊介绍:
International in coverage, Mycologia presents recent advances in mycology, emphasizing all aspects of the biology of Fungi and fungus-like organisms, including Lichens, Oomycetes and Slime Molds. The Journal emphasizes subjects including applied biology, biochemistry, cell biology, development, ecology, evolution, genetics, genomics, molecular biology, morphology, new techniques, animal or plant pathology, phylogenetics, physiology, aspects of secondary metabolism, systematics, and ultrastructure. In addition to research articles, reviews and short notes, Mycologia also includes invited papers based on presentations from the Annual Conference of the Mycological Society of America, such as Karling Lectures or Presidential Addresses.