Contents

• Downloads
  • RiboGrove release 22.228
  • RiboGrove release archive
  • Release notes
• Statistical summary
  • RiboGrove size
  • 16S rRNA gene lengths
  • 16S rRNA gene copy number
  • Top-10 longest 16S rRNA genes
  • Top-10 shortest 16S rRNA genes
  • Top-10 genomes with the largest 16S rRNA copy numbers
  • Top-10 genomes with the highest intragenomic variability of 16S rRNA genes
  • Coverage of primer pairs for different V-regions of bacterial 16S rRNA genes

Downloads

RiboGrove release 22.228 (2025-01-14)

The release is based on RefSeq release 228.

• A fasta file of full-length 16S gene sequences. Download (gzipped fasta file, 9.80 MB)
• Metadata Download (zip archive 6.39 MB)
  
  What information exactly does the metadata contain?

  The metadata consists of the following files:

  1. discarded_sequences.fasta.gz
     This is a fasta file of sequences, which were present in source RefSeq genomes and were annotated a 16S rRNA genes but which have been discarded according to their incompleteness, internal repeats etc. and thus haven’t been included into RiboGrove.
  2. source_RefSeq_genomes.tsv
     This is a TSV files, which contains information about what genomes were used for the RiboGrove construction.
  3. gene_seqs_base_counts.tsv, discarded_gene_seqs_base_counts.tsv
     These are TSV files, which contain nucleotide composition and size of the gene sequences. The first file describes final RiboGrove gene sequences, the second file describes discarded sequences.
  4. categories.tsv
     This is a TSV file, which contains information about what genome categories were assigned to each genome and why. Moreover, it contains information about what sequencing technology was used to sequence each genome.
  5. taxonomy.tsv
     This is a TSV file, which contains taxonomic affiliation of each genome and gene.
  6. intragenic_repeats.tsv
     This is a TSV file, which contains information about intragenomic repeats found in gene sequences using RepeatFinder.
  7. entropy_summary.tsv
     This is a TSV file, which contains summary of instragenomic variability of the 16S rRNA genes. Intragenomic variability are calculated only for the category 1 genomes having more than one 16S rRNA gene. Intragenomic variability is evaluated using Shannon entropy. We align gene sequences from each genome using MAFFT, and then we calculate Shannon entropy for each multiple alignment column (i.e. base).
  8. 16S_GCNs.tsv
     This is a TSV file of 16S rRNA Gene Copy Numbers for each genome in the release.
  9. primer_pair_genomic_coverage.tsv
     This is a TSV file which contains genomic coverage of primer pairs targeting different V-regions of 16S rRNA genes. For example, for Enterobacteriaceae, genomic coverage of a primer pair is the percent of Enterobacteriaceae genomes which contain at least one 16S rRNA gene that can (theoretically) produce a PCR product using the primer pair.

The fasta file is compressed with gzip, and the metadata file is a zip archive. To uncompress them, Linux and Mac OS users may use gzip and zip programs, they should be built-in. For Windows users, the free and open-source (de)compression program 7-Zip is available.

RiboGrove release archive

You can find all releases in the RiboGrove release archive.

Release notes

Starting with RiboGrove 22.228,

1. We publish coverage values for PCR primers pairs commonly used to amplify V-regions of archaeal 16S rRNA genes. See the section “Coverage of primer pairs...” below.
2. Metadata does not contain tables gene_seqs_statistics.tsv and discarded_gene_seqs_statistics.tsv, because they contain much redundant data: taxonomy and genome categories. This data is in the separate tables: taxonomy.tsv and categories.tsv. In place of the removed files, metadata now contains files gene_seqs_base_counts.tsv and discarded_gene_seqs_base_counts.tsv. One can still make a gene_seqs_statistics.tsv table using the script merge_bases_categories_taxonomy.py from ribogrove-tools.

You can find notes to all RiboGrove releases on the release notes page.

Statistical summary

^* Metrics marked with an asterisk were calculated with preliminary normalization, i.e. median within-species gene length was used for the summary.

^* These are median within-species copy numbers.

^* Entropy is Shannon entropy calculated for each column of the multiple sequence alignment (MSA) of all full-length 16S rRNA genes of a genome. Entropy is then summed up (column “Sum of entropy”) and averaged (column “Mean entropy”).

^** Halomicrobium sp. ZPS1 is a quite remarkable case. This genome harbours two 16S rRNA genes, therefore entropy is equal to the number of mismatching nucleotides between sequences of the genes. Respectively, percent of identity between these two gene sequences is 90.70%! This is remarkable because the usual (however arbitrary) genus demarcation threshold of percent of identity is 95%.

Coverage^* of primer pairs for different V-regions of 16S rRNA genes

^* Coverage of a primer pair is the percent of genomes having at least one 16S rRNA gene which can be amplified by PCR using this primer pair. For details, see our paper about RiboGrove.

In the tables below, you can find coverage of primer pairs that are being commonly used to amplify bacterial and archaeal genes (“bacterial” and “archaeal” primers).

You can find a more detailed table in the file primer_pair_genomic_coverage.tsv in the metadata. That table contains coverage not just for phyla, but also for each class, order, family, genus, and species. Moreover, that table contains coverage values for primer pair 1115F–1492R (V7–V9 region). In the tables below, it is omitted for brevity.

RiboGrove, 2025-03-14