Sökning: WFRF:(Stamatakis Alexandros)
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Long-read metabarco...
Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
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- Jamy, Mahwash (författare)
- Uppsala universitet,Systematisk biologi,Science for Life Laboratory, SciLifeLab
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- Foster, Rachel (författare)
- Nat Hist Museum, Dept Life Sci, London, England
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- Barbera, Pierre (författare)
- Heidelberg Inst Theoret Studies, Computat Mol Evolut Grp, Heidelberg, Germany
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- Czech, Lucas (författare)
- Heidelberg Inst Theoret Studies, Computat Mol Evolut Grp, Heidelberg, Germany
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- Kozlov, Alexey (författare)
- Heidelberg Inst Theoret Studies, Computat Mol Evolut Grp, Heidelberg, Germany
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- Stamatakis, Alexandros (författare)
- Heidelberg Inst Theoret Studies, Computat Mol Evolut Grp, Heidelberg, Germany;Karlsruhe Inst Technol, Inst Theoret Informat, Karlsruhe, Germany
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- Bending, Gary (författare)
- Univ Warwick, Sch Life Sci, Coventry, W Midlands, England
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- Hilton, Sally (författare)
- Univ Warwick, Sch Life Sci, Coventry, W Midlands, England
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- Bass, David (författare)
- Nat Hist Museum, Dept Life Sci, London, England;Cefas, Weymouth, England
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- Burki, Fabien (författare)
- Uppsala universitet,Systematisk biologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2019-11-29
- 2020
- Engelska.
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 20:2, s. 429-443
- Relaterad länk:
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http://wrap.warwick....
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- High-throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long-read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an 4500-bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high-quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Nyckelord
- metabarcoding
- PacBio
- phylogeny
- protists
- rDNA operon
- taxonomy
Publikations- och innehållstyp
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- art (ämneskategori)
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- Av författaren/redakt...
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Jamy, Mahwash
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Foster, Rachel
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Barbera, Pierre
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Czech, Lucas
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Kozlov, Alexey
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Stamatakis, Alex ...
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visa fler...
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Bending, Gary
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Hilton, Sally
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Bass, David
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Burki, Fabien
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visa färre...
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Uppsala universitet