diversity Article Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis Marios Nikolaidis 1, Dimitris Mossialos 2 , Stephen G. Oliver 3 and Grigorios D. Amoutzias 1,* 1 Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
[email protected] 2 Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
[email protected] 3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK;
[email protected] * Correspondence:
[email protected]; Tel.: +30-2410-565-289; Fax: +30-2410-565-290 Received: 22 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P.