Improved 18S and 28S rDNA primer sets for NGS-based parasite detection
| Autor: | Haruhiko Maruyama, Akemi Yoshida, Asuka Kounosu, Taisei Kikuchi, Kazunori Murase |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
In silico 030106 microbiology lcsh:Medicine Computational biology Biology Polymerase Chain Reaction 18S ribosomal RNA Article law.invention 03 medical and health sciences law RNA Ribosomal 16S RNA Ribosomal 18S Parasite hosting Animals Parasites lcsh:Science Gene Polymerase chain reaction DNA Primers Multidisciplinary Massive parallel sequencing lcsh:R Eukaryota High-Throughput Nucleotide Sequencing 030104 developmental biology Bacterial 16S rRNA lcsh:Q Parasitology Metagenomics Primer (molecular biology) |
| Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-12 (2019) |
| ISSN: | 2045-2322 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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