Phylogenetic placement of Pseudoneobacillus sp. JJ-79 within Bacillaceae family

This repository contains phylogenetic trees (and associated sequence data) inferred to assess the phylogenetic placement of Pseudoneobacillus sp. JJ-79 (tax id: 2880968) within 512 type strains representative of the Bacillaceae family.

Three phylogenetic trees were inferred, each from a multi-gene dataset (as described at http://giphy.pasteur.fr/PhyloM/Bacillaceae):

• BM1: 87 conserved genes (Wu et al. 2013, Gupta et al. 2020, Patel and Gupta 2020),
• BM2: major subunits of the DNA Gyrase (GyrA and GyrB) and RNA polymerase (RpoB and RpoC; Patel and Gupta 2020),
• BM3: DNA helicase II and DNA polymerase I (UvrD and PolA; Patel and Gupta 2020).

For each dataset BMi (i = 1, 2, 3), four files are available:

• BMi.faa         the concatenation of the filtered multiple sequence alignments (FASTA format);
• BMi.nwk         a maximum likelihood phylogenetic tree inferred from BMi.faa (NEWICK format);
• BMi.pdf         a graphical representation of the phylogenetic tree (PDF format);
• BMi.seq.tar.gz  for each gene name, three FASTA files are available in this tar.gz archive:
  • initial sequences (*.faa),
  • multiple sequence alignment (*.afa),
  • filtered multiple sequence alignment (*.ffa).

In complement, the multiple sequence alignments of 11 loci are available in the archive CSI.tar.gz. Each of these loci shares a conservative signature indel (CSI) that is indicative of the closely related Neobacillus genus (see Table 4 —Niacini clade— in Patel and Gupta 2020):

• fliF, flagellar M-ring protein FliF;
• rplX, 50S ribosomal protein L24;
• prmA, 50S ribosomal protein L11 methyltransferase;
• hisH, imidazole glycerol phosphate synthase subunit HisH;
• hisZ, ATP phosphoribosyltransferase regulatory subunit;
• mdoB, LTA synthase family protein;
• topA, type I DNA topoisomerase;
• pncB, nicotinate phosphoribosyltransferase;
• thiD, phosphomethylpyrimidine kinase;
• recJ, single-stranded-DNA-specific exonuclease RecJ;
• dxs, 1-deoxy-D-xylulose-5-phosphate synthase.