DOI: 10.5061/dryad.dm82j
title: Data from: Pan-genome and phylogeny of Bacillus cereus sensu lato

description: Background: Bacillus cereus sensu lato (s. l.) is an ecologically diverse
 bacterial group of medical and agricultural significance. In this study, I
 use publicly available genomes to characterize the B. cereus s. l.
 pan-genome and perform the largest phylogenetic and population genetic
 analyses of this group to date in terms of the number of genes and taxa
 included. With these fundamental data in hand, I identify genes associated
 with particular phenotypic traits (i.e., "pan-GWAS" analysis),
 and quantify the degree to which taxa sharing common attributes are
 phylogenetically clustered. Methods: A rapid k-mer based approach (Mash)
 was used to create reduced representations of selected Bacillus genomes,
 and a fast distance-based phylogenetic analysis of this data (FastME) was
 performed to determine which species should be included in B. cereus s. l.
 The complete genomes of eight B. cereus s. l. species were annotated de
 novo with Prokka, and these annotations were used by Roary to produce the
 B. cereus s. l. pan-genome. Scoary was used to associate gene presence and
 absence patterns with various phenotypes. The orthologous protein sequence
 clusters produced by Roary were filtered and used to build HaMStR
 databases of gene models that were used in turn to construct phylogenetic
 data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML,
 PAUP, and SplitsTree. Bayesian model-based population genetic analysis
 assigned taxa to clusters using hierBAPS. The genealogical sorting index
 was used to quantify the phylogenetic clustering of taxa sharing common
 attributes. Results: The B. cereus s. l. pan-genome currently consists of
 ≈60,000 genes, ≈600 of which are "core" (common to at least 99%
 of taxa sampled). Pan-GWAS analysis revealed genes associated with
 phenotypes such as isolation source, oxygen requirement, and ability to
 cause diseases such as anthrax or food poisoning. Extensive phylogenetic
 analyses using an unprecedented amount of data produced phylogenies that
 were largely concordant with each other and with previous studies.
 Phylogenetic support as measured by bootstrap probabilities increased
 markedly when all suitable pan-genome data was included in phylogenetic
 analyses, as opposed to when only core genes were used. Bayesian
 population genetic analysis recommended subdividing the three major clades
 of B. cereus s. l. into nine clusters. Taxa sharing common traits and
 species designations exhibited varying degrees of phylogenetic clustering.
description: B. cereus sensu lato
 HaMStR databasesContains the four B.
 cereus s. l. HaMStR databases used in this study. Each HaMStR database
 contains BLAST databases, FASTA files, protein and CDS alignments, and
 HMMs.B_cereus_sensu_lato_HaMStR_dbs.zipB. cereus sensu lato data matricesContains the Bacillus Mash distance matrix, the B. cereus s. l. pan-genome binary data matrix, and the six B. cereus s. l. concatenated data matrices used in the study along with associated RAxML partition specifications.B_cereus_sensu_lato_data_matrices.zipB. cereus sensu lato phylogenetic treesContains the Bacillus FastME tree, the B. cereus s. l. accessory binary tree produced by Roary, the RAxML maximum likelihood trees (ML_1–ML_8), and the PAUP maximum parsimony tree (MP_1).B_cereus_sensu_lato_trees.zipcreate_data_matrix Perl scriptThe create_data_matrix Perl script aligns orthologous protein groups produced by HaMStR, converts alignments to CDS equivalents, applies the consensus method, and concatenates individual gene alignments to produce the final data matrix.create_data_matrix.pl