Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

Summary Ribosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large‐scale exploration of environmental microbial diversity through metabarcoding approaches has been focused mainly on the V...

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Bibliographic Details
Published in:Environmental microbiology 2022-07, Vol.24 (7), p.2979-2993
Main Authors: Sandin, Miguel M., Romac, Sarah, Not, Fabrice
Format: Article
Language:English
Subjects:
DNA
DNA barcoding
Environmental DNA
Environmental Sciences
Environmental surveys
Gene sequencing
Genomics
Microorganisms
Nucleotide sequence
PCR
Phylogenetics
Phylogeny
Radiolaria
rRNA 18S
Sequencing
Variability
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Summary:Summary Ribosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large‐scale exploration of environmental microbial diversity through metabarcoding approaches has been focused mainly on the V4 and V9 regions of the 18S rRNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra‐genomic variability). Here we explored the intra‐genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra‐genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with
ISSN:1462-2912
1462-2920
1462-2920
DOI:10.1111/1462-2920.16081