Minimal Genomes Simplify the Analysis of Biological Relationships in Medicine, Taxonomy, Ecology, and Astrobiology
Master of Science in Biology (MS)
Combrink, Keith D.
Kidd, Michael R.
Ynalvez, Ruby A.
As humans, we continuously thrive to determine meaningful biological relationships between living things on the basis of specific characteristics. Taxonomy is the science that studies these connections for the purpose of naming and grouping organisms as well as identifying logical clusters (i.e, clade). Its origin may be traced as far back as ancient Greece and beyond, and while we explore species diversity, most of our attention focuses on the biomedical and ecological applications of taxonomy. The contemporary taxonomical revolution began with Carl Linnaeus. He established the principles of binomial nomenclature and taxonomical hierarchy that we employ now. Relationships were later drawn as tree diagrams whose order described the evolutionary development of species but the branch distances didn’t accurately reflect time. With Charles Darwin, genetics started to play a larger role in taxonomy, and cladograms were determined using relatedness. The rise of bioinformatics in the last century facilitated to calculate species divergence, resulting in accurate visuals of complex branch distances in the form of phylogenetic trees. Finally, the genomics revolution provided a wealth of information, but its sheer endless amount of data has been challenging to process. As a consequence, our ability to unfold the mysteries of biological evolution remain limited by technology since multi-species comparisons remain computationally intensive. To solve this problem, we used a new computational approach that is based on the analysis of organisms with small genomes to construct evolutionary relationships. Minimal genomes contain mostly the core set of genes, allowing the investigation of the origin of life, evolutionary connections, and potential antibiotic targets. By comparing genomics data of minimal genomes from all sequenced phyla, we observed that these organisms reflect the diversity of their genomically larger counterparts including GC content, proteins per megabase (Mb), and 16S rRNA relationships. Thus, minimal genomes are suitable to use in taxonomy studies. We also compared the 16S rRNA of all species of the phylum Tenericutes as described in the Bergey’s Manual as well as the proteomes from all mammalian Mycoplasma species. The Tenericutes, commonly known as “mycoplasmas,” are bacteria that lack a cell wall, have notoriously small genomes, and are AT rich. Our results demonstrated that phylogenies at small scales are alarmingly contingent upon the sequence alignment algorithms that is used. In addition, comparison of the 16S rRNA of all Tenericutes revealed that these organisms are paraphyletic. Proteome alignments found computed homologs lacking. However, 16S rRNA data combined with statistics on host range, geographical distribution, and habitat (e.g., host organ system) revealed that there are common features within the clades that may be helpful for taxonomy studies. Furthermore, our data supports the intention of other scientists to reorganize the taxonomy of the Mycoplasmatales order and its type species. Minimal genomes are therefore a source of untapped potential.
Deliz Aguirre, Rafael, "Minimal Genomes Simplify the Analysis of Biological Relationships in Medicine, Taxonomy, Ecology, and Astrobiology" (2021). Theses and Dissertations. 125.