Search: onr:"swepub:oai:DiVA.org:uu-390901" >
Confident phylogene...
-
Martijn, JoranUppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab
(author)
Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon
- Article/chapterEnglish2019
Publisher, publication year, extent ...
-
2019-05-07
-
John Wiley & Sons,2019
-
electronicrdacarrier
Numbers
-
LIBRIS-ID:oai:DiVA.org:uu-390901
-
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-390901URI
-
https://doi.org/10.1111/1462-2920.14636DOI
Supplementary language notes
-
Language:English
-
Summary in:English
Part of subdatabase
Classification
-
Subject category:ref swepub-contenttype
-
Subject category:art swepub-publicationtype
Notes
-
Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286-37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (similar to 1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
-
Lind, Anders E.Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab(Swepub:uu)andli580
(author)
-
Schön, Max E.Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab(Swepub:uu)maxsc705
(author)
-
Spiertz, IanUppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär evolution(Swepub:uu)iansp788
(author)
-
Juzokaite, LinaUppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab(Swepub:uu)linju307
(author)
-
Bunikis, IgnasUppsala universitet,Science for Life Laboratory, SciLifeLab(Swepub:uu)ignbu776
(author)
-
Pettersson, Olga V.Uppsala universitet,Science for Life Laboratory, SciLifeLab(Swepub:uu)olvin020
(author)
-
Ettema, Thijs J. G.Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab,Wageningen Univ, Dept Agrotechnol & Food Sci, Lab Microbiol, NL-6708 WE Wageningen, Netherlands(Swepub:uu)thiet468
(author)
-
Uppsala universitetMolekylär evolution
(creator_code:org_t)
Related titles
-
In:Environmental Microbiology: John Wiley & Sons21:7, s. 2485-24981462-29121462-2920
Internet link
Find in a library
To the university's database