Host-adaptation in Legionellales is 1.9 Gya, coincident with eukaryogenesis

This dataset contains genomes, proteomes and protein alignments mentioned in Hugoson et al (2021). It has been used to analyze the evolution of host-adaptation in the order Legionellales.

The data is organized by dataset type, and then by dataset.

The four datasets used here are

• Gamma105, comprising 105 Gammaproteobacteria and 5 outgroups;
• Legio93, comprising 93 Legionellales and 20 outgroups;
• Bacteria134, built on Gamma105, adding 27 genomes from Betts et al. (2018)
• Bacteria93, built by removing Legionella, Francisella, Fangia and Piscirickettsia genera from Bacteria134

1_genomes
Genomes as downloaded or assembled

• 1_1_Gamma105
• 1_2_Legio93

2_proteomes
Proteomes, as annotated by prokka

• 2_1_Gamma105
• 2_2_Legio93
• 2_3_Bacteria134

3_alignments

In the first three and the fifth folders, the following files are found. All sequence and alignment files are in fasta format:

• *_concatenated.fasta: concatenated alignment, trimmed.
• *.map: map of the files, tab-separated. The first row is a title row. The three first columns give the organism, the marker and the id (as found in the fasta file) for the protein.
• *_unaligned: non-aligned sequences for each marker.
• *_aligned: aligned sequences, for each marker. The prefix gives the software used for the alignment.
• *_trimmed: aligned, trimmed sequences for each marker. The prefix gives the software used to trim the alignment.

• 3_1_Gamma105: Based on the Bact109 set of markers.
• 3_2_Legio93: Based on the Bact109 set of markers.
• 3_3_Bacteria134: Based on Gamma105 set and Bact109 set of markers.
• 3_4_Bacteria93: Based on Bacteria134 (removed fast-evolving genomes).
• 3_5_TB4SS_auto: Alignment of 12 genes of the T4BSS, automatically detected in all genomes. 
• 3_6_TB4SS_manual: Alignment of 25 genes of the T4BSS, manually curated by collinearity analysis.