The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.
DNA metabarcoding
amplicon sequencing
environmental sequencing
reference sequences
ribosomal DNA
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
21 Oct 2024
21 Oct 2024
Historique:
revised:
27
06
2024
received:
27
04
2024
accepted:
27
09
2024
medline:
21
10
2024
pubmed:
21
10
2024
entrez:
21
10
2024
Statut:
aheadofprint
Résumé
Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.
Identifiants
pubmed: 39428982
doi: 10.1111/1755-0998.14031
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e14031Subventions
Organisme : The University of Oslo
Informations de copyright
© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.
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