Anete Borodušķe , Juris Ķibilds , Dāvids Fridmanis , Dita Gudrā , Maija Ustinova , Māris Seņkovs , Vizma Nikolajeva
{"title":"宿主植物DNA的肽核酸(PNA)钳位是否有利于真菌内生菌群落基于ITS1扩增子的表征?","authors":"Anete Borodušķe , Juris Ķibilds , Dāvids Fridmanis , Dita Gudrā , Maija Ustinova , Māris Seņkovs , Vizma Nikolajeva","doi":"10.1016/j.funeco.2022.101181","DOIUrl":null,"url":null,"abstract":"<div><p>Fungal endophyte community amplicon sequencing can lose a significant number of informative reads due to host-plant co-amplification. Blocking of plant-specific sequences with peptide nucleic acid (PNA) clamps has been shown to improve metrics of detected microbial diversity in studies targeting 16S and 18S regions of rRNA genes. However, PNA clamping has not been applied to the plant <em>ITS</em> region of <em>rRNA</em> gene – a widely accepted fungal marker. By applying PNA clamping technique to <em>ITS</em> amplicon sequencing of the endophytic fungal community of elderberry this study shows that PNA clamping significantly reduces host-plant co-amplification with the universal ITS1/ITS4 primer set. However, PNA clamping in combination with the discriminatory ITS1F/ITS2 primer set did not improve the metrics of fungal endophyte community <em>ITS</em> amplicon Illumina sequencing. This study shows that PNA clamping does not add practical benefit to taxonomic profiling of plant-associated fungal communities if the primers are already specific enough to exclude amplification of host DNA.</p></div>","PeriodicalId":55136,"journal":{"name":"Fungal Ecology","volume":null,"pages":null},"PeriodicalIF":1.9000,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Does peptide-nucleic acid (PNA) clamping of host plant DNA benefit ITS1 amplicon-based characterization of the fungal endophyte community?\",\"authors\":\"Anete Borodušķe , Juris Ķibilds , Dāvids Fridmanis , Dita Gudrā , Maija Ustinova , Māris Seņkovs , Vizma Nikolajeva\",\"doi\":\"10.1016/j.funeco.2022.101181\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Fungal endophyte community amplicon sequencing can lose a significant number of informative reads due to host-plant co-amplification. Blocking of plant-specific sequences with peptide nucleic acid (PNA) clamps has been shown to improve metrics of detected microbial diversity in studies targeting 16S and 18S regions of rRNA genes. However, PNA clamping has not been applied to the plant <em>ITS</em> region of <em>rRNA</em> gene – a widely accepted fungal marker. By applying PNA clamping technique to <em>ITS</em> amplicon sequencing of the endophytic fungal community of elderberry this study shows that PNA clamping significantly reduces host-plant co-amplification with the universal ITS1/ITS4 primer set. However, PNA clamping in combination with the discriminatory ITS1F/ITS2 primer set did not improve the metrics of fungal endophyte community <em>ITS</em> amplicon Illumina sequencing. This study shows that PNA clamping does not add practical benefit to taxonomic profiling of plant-associated fungal communities if the primers are already specific enough to exclude amplification of host DNA.</p></div>\",\"PeriodicalId\":55136,\"journal\":{\"name\":\"Fungal Ecology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2023-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Fungal Ecology\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1754504822000423\",\"RegionNum\":3,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"ECOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Fungal Ecology","FirstCategoryId":"93","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1754504822000423","RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"ECOLOGY","Score":null,"Total":0}
Does peptide-nucleic acid (PNA) clamping of host plant DNA benefit ITS1 amplicon-based characterization of the fungal endophyte community?
Fungal endophyte community amplicon sequencing can lose a significant number of informative reads due to host-plant co-amplification. Blocking of plant-specific sequences with peptide nucleic acid (PNA) clamps has been shown to improve metrics of detected microbial diversity in studies targeting 16S and 18S regions of rRNA genes. However, PNA clamping has not been applied to the plant ITS region of rRNA gene – a widely accepted fungal marker. By applying PNA clamping technique to ITS amplicon sequencing of the endophytic fungal community of elderberry this study shows that PNA clamping significantly reduces host-plant co-amplification with the universal ITS1/ITS4 primer set. However, PNA clamping in combination with the discriminatory ITS1F/ITS2 primer set did not improve the metrics of fungal endophyte community ITS amplicon Illumina sequencing. This study shows that PNA clamping does not add practical benefit to taxonomic profiling of plant-associated fungal communities if the primers are already specific enough to exclude amplification of host DNA.
期刊介绍:
Fungal Ecology publishes investigations into all aspects of fungal ecology, including the following (not exclusive): population dynamics; adaptation; evolution; role in ecosystem functioning, nutrient cycling, decomposition, carbon allocation; ecophysiology; intra- and inter-specific mycelial interactions, fungus-plant (pathogens, mycorrhizas, lichens, endophytes), fungus-invertebrate and fungus-microbe interaction; genomics and (evolutionary) genetics; conservation and biodiversity; remote sensing; bioremediation and biodegradation; quantitative and computational aspects - modelling, indicators, complexity, informatics. The usual prerequisites for publication will be originality, clarity, and significance as relevant to a better understanding of the ecology of fungi.