This is the home for the Ribosomal Operon Database (ROD).
The database contains full-length eukaryotic ribosomal operons. The database is based on the genome assemblies from NCBI, and the operons are extracted from the assemblies. The database currently contains 69,480 operon variants from more than 11,935 genomes.
The database is publised in Molecular Ecology Resources. Please cite the paper if you use the database.
Krabberød, A. K., Stokke, E., Thoen, E., Skrede, I., & Kauserud, H. (2024). The Ribosomal Operon Database: A Full‐Length rDNA Operon Database Derived From Genome Assemblies. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.14031
The current release is ROD v1.2 - Golden Rod
NEWS! The work has been started to integrate ROD with PR2. It is expected to be included in the next version.
The database contains full-length ribosomal operons extracted from genome assemblies. The database is based on the genome assemblies from NCBI, and the operons are extracted from the assemblies. The database currently contains 69,480 operon variants from more than 11,935 genomes.
There are three files associated with the database (all in flat tab-separated format, and as .rds objects for R):
- Genome Statistics: statistics based on the genome assemblies. Contains the number of copies pr. genome, the number of operon variants (see paper for definition), length distribution and genetic distance statistics.
- Operon variants: statistics based on the variant from the genomes, i.e. it has multiple entries for the genomes with multiple variants, one for each variant.
For an interactive Krona plot of the genomes in the data base see here Krona plot
- The paper is now published in Molecular Ecology Resources. Please cite the paper if you use the database.
- We are currently integrating ROD with PR2, and it will be included in the next PR2 release.
- Updated to ROD v1.2
- Corrected wrongly spelled Oochrophyta to the correct Ochrophyta.
- Added a new column to the operon variants file with an annotation stating operon is in the reference dataset or not.
- Added the metadata from NCBI.
- Add explanations for all the statistics and columns in the files.
- Add scripts used in the paper to calculate statistics and make figures
- Updated to Version v1.1
- Corrected taxonomy for 8 entries of Cryptococcus with a wrong subdivision_ assignment.
- Updated to Version v1.0
- Plans for the next version (nicknamed ROD Stewart): update and clean some of the taxonomy and provide more statistics.
- We also have plans for testing different clustering strategies to see how real Operons when treated with common clustering approaches used in many metabarcoding studies.
- ROD is born. 69k glorious whole operons sequence variants from 11k genomes in their full length! More stats coming...
- Fasta and a Tibble in .rds format ba
- (Early February 2024) The first version of the database has been uploaded ROD v0.3. For now, it is a fasta file with ribosomal sequences, and all the info is in the header. This version contains a set of near-full-length ribosomal operons. It contains 104k operons, representing 16k genomes fished from 35k downloaded from NCBI. The operons span at least 4000 bp. But some lack the beginning of 18S others the end of 28S (and sadly some lack both).
- The plan for the next release (nicknamed v0.4 GoldenROD) is to remove lacking the beginning or the end. The initial analysis of ROD seems to indicate that about 33% of the operons are missing portions in either '3 or '5. The updated number of full-length operons is 69K from 12K genome.
The main source for data is the genome assemblies from NCBI, downloaded Medio 2023:
# To download the meta data:
rsync -t -v rsync://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt .
Overview of genomes in NCBI as of Dec. 2023
## See rsync://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
## This is from column 25:
16572 fungi
6249 invertebrate
7232 metagenome # Not included in ROD
7593 other # Not included in ROD
3604 plant
1978 protozoa
2854 vertebrate_mammalian
3746 vertebrate_other
80657 viral # Not included in ROD
16538 archaea # Not included in ROD
1779617 bacteria # Not included in ROD
"All the keywords in this explanation, by the way, are totally misleading due to the everyday quirks of language " - Don DeLillo, Ratner's Star