DOI: 10.5061/dryad.v41ns1s7g
title: Taxonomic reassessment of genomes from a divergent population of Streptococcus suis by average nucleotide identity analysis

description: This dataset provides genomic-level re-identification and taxonomic
 reassessment of Streptococcus suis out-population strains based on average
 nucleotide identity (ANI), 16S rRNA gene comparisons, and other
 phylogenetic markers. The dataset includes an Excel workbook with eight
 sheets (Sheet A–H), which together constitute Supplementary Table S1. This
 table contains detailed information on the studied strains, including
 their disease association, sequence alignment results (identity, coverage,
 and length) of 16S rRNA genes against both the S. suis type strain S735
 and a database of prokaryotic type strains, ANI and AAI values compared to
 S735, accession numbers for short-read and long-read data, genome assembly
 IDs, phylogenetic lineage within the S. suis tree, group classification
 within the out-population, and cluster medoid status indicating
 representative strains. Through comparative genomic analysis, this study
 established an ANI threshold of 93.17% for defining authentic S. suis,
 revealing that all 645 genomes from the out-population fell below this
 cutoff and thus did not belong to S. suis. Further pairwise ANI comparison
 identified 18 distinct clusters among these strains, leading to the
 proposal of 12 novel Streptococcus species and the reclassification of six
 as known species. This dataset serves as a valuable resource for
 researchers studying streptococcal taxonomy, zoonotic pathogens, and
 bacterial evolution. It enables further investigations into genomic
 diversity, species delineation, and the evolutionary relationships within
 the genus Streptococcus.
description: The analysis primarily employed ANI (Average Nucleotide
 Identity), 16S rRNA sequences, and AAI (Average Amino Acid Identity)
 comparisons to calculate relevant information for the entire
 <em>Streptococcus suis</em> out-population as well as the type
 strains of known species within the genus
 <em>Streptococcus</em>.
description: # Taxonomic reassessment of genomes from a divergent population of
 Streptococcus suis by average nucleotide identity analysis Dataset DOI:
 [10.5061/dryad.v41ns1s7g](10.5061/dryad.v41ns1s7g) ## Description of the
 data and file structure The table contains information on the
 re-identification of *Streptococcus suis* out-population species at the
 genomic level. It includes disease-related information of the studied
 strains, as well as ANI (Average Nucleotide Identity), 16S rRNA, and other
 comparison data. The table consists of eight sheets, labeled A through H.
 ### Files and variables #### File: S1.xlsx **Description:** The table
 contains information on the re-identification of *Streptococcus suis*
 out-population species at the genomic level. It includes disease-related
 information of the studied strains, as well as ANI (Average Nucleotide
 Identity), 16S rRNA, and other comparison data. The table consists of
 eight sheets, labeled A through H. * **Sheet A**: Basic information of
 *Streptococcus suis* outgroup strains, including 16S rRNA gene sequences
 and ANI (Average Nucleotide Identity) comparison results. * **Sheet B**:
 ANI clustering results of *Strectococcus suis* outgroup1 strains. *
 **Sheet C**: ANI comparison values between *Streptococcus suis* outgroup1
 strains and the type strains of known *Streptococcus* species. * **Sheet
 D**: ANI clustering results of *Streptococcus suis* outgroup3 strains. *
 **Sheet E**: ANI comparison values between *Streptococcus suis* outgroup3
 strains and the type strains of known *Streptococcus* species. * **Sheet
 F**: ANI comparison values between *Streptococcus suis* outgroup2 strains
 and the type strains of known *Streptococcus* species. * **Sheet G**: ANI
 clustering results of *Streptococcus suis* outgroup4 strains. * **Sheet
 H**: ANI comparison values between *Streptococcus suis* outgroup4 strains
 and the type strains of known *Streptococcus* species. * The column names
 and descriptions are as follows:        **sheet A:** * **Filename**: The
 filename of the genomic data used in the analysis. * **Streptococcus suis
 S735**: Extract the complete 16S sequence, i.e., align with Streptococcus
 suis S735; use "unavailable" if not extracted; use
 "NA" if the strain sequence is not available in NCBI. * **pIdent
 (line C):** Sequence identity percentage of the 16S rRNA gene when
 compared to the *Streptococcus suis* type strain S735. * **qcovs (line
 D)**: Alignment coverage percentage of the 16S rRNA gene when compared to
 the *Streptococcus suis* type strain S735. * **length (line E)**: Length
 (in base pairs) of the aligned region when comparing the 16S rRNA gene to
 the *Streptococcus suis* type strain S735. * **16S-subject**: Sequence
 identity percentage of the 16S rRNA gene when compared to a database of
 prokaryotic type strains. * **pIdent (lineG):** Sequence identity
 percentage of the 16S rRNA gene when compared to the prokaryotic type
 strains database. * **qcovs (line H)**: Alignment coverage percentage of
 the 16S rRNA gene when compared to the prokaryotic type strains database.
 * **length (line I)**: Length (in base pairs) of the aligned region when
 comparing the 16S rRNA gene to the prokaryotic type strains database. *
 **ANI Final identification**: The species identification results
 determined by ANI alignment in this study. * **ANI with S735**: Average
 Nucleotide Identity value when compared to the *Streptococcus suis* type
 strain S735. * **AAI with S.suis S735**: Average Amino Acid Identity value
 when compared to the *Streptococcus suis* type strain S735. * **Bioproject
 ID (short-read data)**: Bioproject ID associated with the short-read
 sequencing data of the strain. * **Bioproject ID (long-read data)**:
 Bioproject ID associated with the long-read sequencing data of the strain.
 * **Genome Assembly**: Accession number or identifier for the genome
 assembly of the strain. * **Lineage**: Phylogenetic lineage of the strain
 within the *Streptococcus suis* species. * **Group**: The specific
 outgroup cluster or group to which the strain belongs. **sheet B:** *
 **Species:** Name of the species involved in the alignment. * **Genome:**
 Name of the genome. * **Cluster_Medoid**: Indicates whether the strain is
 the medoid (representative strain) of its cluster, based on computational
 analysis. **sheet C:** * **Query:** Name of the genome involved in the
 alignment. * **Reference:** Known type strain of the Streptococcus species
 that the query aligns to. * **ANI (%):** The specific ANI value from the
 alignment. The column names in Tables D–H are explained in reference to
 Tables B and C. * The reasons for unavailable or missing data
 ("NA") in the "A" sheet are as follows: * For the
 columns **"Streptococcus suis S735"** and
 **"16S-subject"**, the missing information is due to the fact
 that the draft genomes did not allow for the extraction of complete 16S
 rRNA gene sequences. * In the columns **"pIdent"**,
 **"qcovs"**, and **"length"**, "NA"
 indicates that no 16S rRNA sequence was available for alignment, and
 therefore no corresponding alignment values could be calculated. * The
 **"Bioproject ID (long-read data)"** column contains
 "NA" when no complete genome assembly or long-read data are
 available in the NCBI database. * The **"Genome Assembly"**
 column contains "NA" when the corresponding genome sequence does
 not have a separate Assembly accession number in NCBI. * The
 **"Lineage"** column contains "NA" for strains
 belonging to the *Streptococcus suis* out population. Lineage
 classification was only assigned for strains within the central population
 in the study. ##### **Abbreviation** ANI (Average Nucleotide Identity) AAI
 (Average Amino Acid Identity) ## Code/software * **Microsoft Excel**
 (recommended) or * **LibreOffice Calc** (free and open-source alternative)
 or * **Google Sheets** (online tool). **Workflow Description**: The
 submitted file is an Excel workbook (`data.xlsx`) containing 8 sheets
 (labeled A through H). Each sheet includes genomic comparison data for
 *Streptococcus suis* strains, such as ANI, AAI, and 16S rRNA alignment
 results. No additional software, scripts, or packages are required to view
 the data. **Instructions for Use**: Simply download the file and open it
 using one of the compatible spreadsheet tools listed above. All data is
 self-contained within the workbook, and no further processing is
 necessary. ## Access information **Links to Other Publicly Accessible
 Locations of the Data**: The data provided in this submission is original
 and has not been previously published or stored in any other publicly
 accessible location. Therefore, no additional links are available.
 **Source(s) of the Data**: All data were generated as part of this study
 and are included in full with this submission. No external sources were
 used in the creation of this dataset.