Improved 18S and 28S rDNA primer sets for NGS-based parasite detection.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

DNA Primers*/chemistry ; DNA Primers*/genetics ; Eukaryota*/classification ; Eukaryota*/genetics ; High-Throughput Nucleotide Sequencing* ; Parasites*/classification ; Parasites*/genetics ; Polymerase Chain Reaction*; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics; Animals

The development and application of next-generation sequencing (NGS) have enabled comprehensive analyses of the microbial community through extensive parallel sequencing. Current analyses of the eukaryotic microbial community are primarily based on polymerase chain reaction amplification of 18S rRNA gene (rDNA) fragments. We found that widely-used 18S rDNA primers can amplify numerous stretches of the bacterial 16S rRNA gene, preventing the high-throughput detection of rare eukaryotic species, particularly in bacteria-rich samples such as faecal material. In this study, we employed in silico and NGS-based analyses of faecal samples to evaluated the existing primers targeting eukaryotic 18S and 28S rDNA in terms of avoiding bacterial read contamination and improving taxonomic coverage for eukaryotes, with a particular emphasis on parasite taxa. Our findings revealed that newly selected primer sets could achieve these objectives, representing an alternative strategy for NGS.

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0 (DNA Primers)
0 (RNA, Ribosomal, 16S)
0 (RNA, Ribosomal, 18S)

Date Created: 20191102 Date Completed: 20201028 Latest Revision: 20210110

20231215

PMC6823512

10.1038/s41598-019-52422-z

31673037