Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century. Issue 7 (July 2021)

• Record Type: Journal Article
• Authors: Koonin, Eugene V.; Makarova, Kira S.; Wolf, Yuri I.
• Is Part Of: Trends in microbiology. Volume 29:Issue 7(2021)
• Page Start: 582
• Page End: 592
• Publication Date: 2021-07
• Subjects: prokaryote genome evolution -- pangenome -- phylogenetic trees -- metagenomics -- single-cell genomics -- gene gain and loss; Microbiology -- Periodicals; Infection -- Periodicals; Virulence (Microbiology) -- Periodicals; Infection -- Periodicals; Microbiology -- Periodicals; Virulence -- Periodicals; Microbiologie -- Périodiques; Infection -- Périodiques; Virulence (Microbiologie) -- Périodiques; Infection; Microbiology; Virulence (Microbiology); 579
• DOI: 10.1016/j.tim.2021.01.005
• Languages: English
• ISSNs: 0966-842X

Abstract

Abstract : Prokaryote genomics started in earnest in 1995, with the complete sequences of two small bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium . During the next quarter century, the prokaryote genome database has been growing exponentially, with no saturation in sight. For most of these 25 years, genome sequencing remained limited to cultivable microbes. Together with next-generation sequencing methods, advances in metagenomics and single-cell genomics have lifted this limitation, providing for an increasingly unbiased characterization of the global prokaryote diversity. Advances in computational genomics followed the progress of genome sequencing, even if occasionally lagging behind. Several major new branches of bacteria and archaea were discovered, including Asgard archaea, the apparent closest relatives of eukaryotes and expansive groups of bacteria and archaea with small genomes thought to be symbionts of other prokaryotes. Comparative analysis of numerous prokaryote genomes spanning a wide range of evolutionary distances changed the conceptual foundations of microbiology, supplanting the notion of species genomes with fixed gene sets with that of dynamic pangenomes and the notion of a single Tree of Life (ToL) with a statistical tree-like trend among individual gene trees. Strides were also made towards a theory and quantitative laws of prokaryote genome evolution. Highlights: The database of prokaryote genomes has been growing exponentially for 25 years. There is no saturation of prokaryote diversity currently in sight. Most prokaryotes have dynamic, 'open' pangenomes. Metagenomics makes key contributions to the study of prokaryote diversity. There is no single Tree of Life but a tree-like trend in evolution is discernible.