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..., Genomes were sequenced at the JGI using Pacific Biosciences (PacBio) technology on either an RSII instrument (P6/C4 chemistry), or Sequel (v2.1 v2 or v3.0 chemistries) or using an Illumina NovaSeq (v1 chemistry) and have been reported previously (https://pubmed.ncbi.nlm.nih.gov/37764097/). All genome sequences were annotated using the JGI IMG pipeline, with the vast majority by version v.5.0.10 and details available for each at the JGI IMG database. Genomes used in this study are curated under the GOLD study ID Gs0118866, with links to raw sequence data available via JGI or via the NCBI SRA database. Contigs were classified into plasmid and chromosomal categories to determine plasmid presence or absence using PlasFlow v1.1.0. For convenience, the 270 sub-projects are deposited under NCBI BioProject PRJNA990349. Strains analyzed in this study are shown Supplementary Table 1, and include relevant culture collection details (Supplementary Tables 2-3). Additional methodological details are ..., , # 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...