Supplementary materials for Phylogenomics and genetic analysis of solvent-producing Clostridium species

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerenckiI, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escheric..., A modified phenol-chloroform extraction based on Annan et al. (2019) was used to purify genomic DNA. Cells were harvested by centrifugation at 6,000 x g for 15 min at 4°C, and washed in 50 mL potassium phosphate buffer (10 mM, pH 7.5). The cells were resuspended in STE buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA; 200 mM sucrose) with 30 μL lysozyme (100 mg/mL), followed by a combination of SDS, EDTA, Tris, RNaseA/T1, and Proteinase K. Each addition was followed by specific incubation steps at 37°C. The lysate was processed using Phase Lock Gel Heavy tubes and a modified phenol::chloroform procedure that employed MaXtract High Density (Qiagen) phase-lock tubes. DNA was precipitated, then washed with -20°C 70% ethanol, dried, and resuspended in heated (60°C) 1x TE buffer (10 mM Tris, pH 8, and 0.1 mM EDTA). Purified DNA underwent 16S rRNA gene sequencing to confirm strain identity before being shipped to the DOE Joint Genome Institute (JGI) for genome sequencing and annotation. Reference: A..., , # Supplementary Dataset and Tables for Phylogenomics and Genetic Analysis of Solvent-Producing *Clostridium* Species

This Dryad submission supports a publication entitled “Phylogenomics and Genetic Analysis of Solvent-Producing *Clostridium* Species” accepted for publication at *Scientific Data* (SDATA-23-01651) in April 2024 ([https://www.nature.com/sdata/)](https://www.nature.com/sdata/\)). The paper describes 270 genome sequences and detailed analyses. The raw sequence and genome sequence information are publicly available, described in the publication and in the related works section of this submission. This Dryad dataset provides supplementary information to the *Scientific Data* publication.

## Description of the data and file structure

There are 11 files in this dataset in excel format:

**Supplementary Table 1**. This file contains 270 DJ strain designations, linked to database references (e.g. GenBank accession numbers, Genome IDs) and provides important genome analysis resu...