Phylogeny Influences Genome Size and GC but not Sequence and Organismal Complexity in Staphylococci

Abstract

Aim: Like other ecological and morphological features, genomic features are adaptive and can be influenced by phylogeny. While some features like genome size and genomic GC have been explored in the past, some features like genomic repeat fraction and protein-coding genes remain unexplored. Understanding the trait evolution of individual genomic features and how these features are related to each other is critical to evolutionary biology.Materials and Methods: This study investigates the trait evolution of genomic features in Staphylococcus, a bacterial clade having many pathogenic species and is of medical and pharmacological interest. Data on genome size, genomic GC content, number of protein-coding genes, and genomic repeat fraction for species in the genus Staphylococcus is collected to study their trait evolution and phylogenetic corrected relationships between them with the help of whole-genome phylogenetic trees. Results and Conclusion: We observe that the four genomic features studied follow differing trait evolution models. Genome sizes and genomic GC content show a strong phylogenetic signal, supporting the early-burst model, while the number of protein-coding genes and genomic repeat fraction show phylogeny-independent trait evolution. There is a significant negative correlation between genome size and genomic GC content, indicating that the addition of AT-rich sequences to the genome drove the increasing genome size during the early burst of diversification in Staphylococcus. The lack of correlation between genome size with genomic repeat fraction and number of coding genes indicates that sequence complexity and organismal complexity evolved independently of genome size evolution in Staphylococci, and repeat expansion may not have contributed to the genome size increase during diversification.

Keywords: Phylogenetic conservation; Phylogenetic signal; Staphylococcus; Trait Evolution