Search: onr:"swepub:oai:gup.ub.gu.se/217166" >
Shotgun metagenomes...
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
-
Tedersoo, Leho (author)
-
Anslan, Sten (author)
-
- Bahram, Mohammad (author)
- Uppsala universitet,Systematisk biologi
-
show more...
-
Põlme, Sergei (author)
-
Riit, Taavi (author)
-
Liiv, Ingrid (author)
-
- Kõljalg, Urmas (author)
- Uppsala universitet,Systematisk biologi
-
Kisand, Veljo (author)
-
- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
-
Hildebrand, Falk (author)
-
Bork, Peer (author)
-
Abarenkov, Kessy (author)
-
show less...
-
(creator_code:org_t)
- 2015-05-13
- 2015
- English.
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 10, s. 1-43
- Related links:
-
https://mycokeys.pen...
-
show more...
-
https://doi.org/10.3...
-
https://uu.diva-port... (primary) (Raw object)
-
https://gup.ub.gu.se...
-
https://doi.org/10.3...
-
https://urn.kb.se/re...
-
show less...
Abstract
Subject headings
Close
- Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
Subject headings
- LANTBRUKSVETENSKAPER -- Veterinärmedicin -- Patobiologi (hsv//swe)
- AGRICULTURAL SCIENCES -- Veterinary Science -- Pathobiology (hsv//eng)
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Jordbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Agricultural Science (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
Keyword
- High-throughput sequencing
- internal transcribed spacer (ITS)
- nuclear large subunit (LSU)
- nuclear small subunit (SSU)
- Illumina MiSeq sequencing
- shotgun metagenomics
- primer bias
- taxonomic coverage
- identification bias
- High-throughput sequencing
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
-
MycoKeys
(Search for host publication in LIBRIS)
To the university's database
- By the author/editor
-
Tedersoo, Leho
-
Anslan, Sten
-
Bahram, Mohammad
-
Põlme, Sergei
-
Riit, Taavi
-
Liiv, Ingrid
-
show more...
-
Kõljalg, Urmas
-
Kisand, Veljo
-
Nilsson, R. Henr ...
-
Hildebrand, Falk
-
Bork, Peer
-
Abarenkov, Kessy
-
show less...
- About the subject
-
- AGRICULTURAL SCIENCES
-
AGRICULTURAL SCI ...
-
and Veterinary Scien ...
-
and Pathobiology
-
- AGRICULTURAL SCIENCES
-
AGRICULTURAL SCI ...
-
and Agriculture Fore ...
-
and Soil Science
-
- AGRICULTURAL SCIENCES
-
AGRICULTURAL SCI ...
-
and Agriculture Fore ...
-
and Agricultural Sci ...
-
- MEDICAL AND HEALTH SCIENCES
-
MEDICAL AND HEAL ...
-
and Basic Medicine
-
and Microbiology in ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Evolutionary Bio ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Biological Syste ...
-
show more...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Ecology
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Bioinformatics a ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Botany
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Microbiology
-
show less...
- Articles in the publication
-
MycoKeys
- By the university
-
University of Gothenburg
-
Uppsala University