Genetic Diversity and Characterization of Circular Replication (Rep)-Encoding Single-Stranded (CRESS) DNA Viruses

Area of Science:

• Virology
• Molecular Biology
• Bioinformatics

Background:

• Cress-DNA viruses are widespread in eukaryotes and crucial for global ecosystems.
• The full genetic diversity of these viruses remains incompletely understood.
• Existing classification relies primarily on the replication (Rep) protein.

Purpose of the Study:

• To elucidate the genetic diversity of replication (Rep) and capsid (Cap) proteins in CRESS-DNA viruses.
• To establish a more comprehensive classification system for CRESS-DNA viruses based on protein domain organization and phylogenetic analysis.
• To investigate the evolutionary pressures shaping the Rep and Cap genes of CRESS-DNA viruses.

Main Methods:

• Utilized CLANS and phylogenetic analyses to cluster Rep and Cap proteins.
• Analyzed the presence and organization of Viral_Rep and P-loop_NTPase domains within Rep proteins.
• Compared clustering patterns of Rep and Cap proteins across different viral families (e.g., Circoviridae, Smacoviridae).

Main Results:

• Rep proteins were classified into 10 clusters, with domain organization varying across groups.
• Cap proteins were divided into 20 distinct clusters for the first time.
• Selection pressure, rather than mutational pressure, was identified as a significant driver of Rep and Cap gene evolution.

Conclusions:

• The study provides a refined classification of CRESS-DNA viruses based on Rep and Cap protein diversity.
• The findings suggest potential for recombination events in Cap and Rep proteins.
• This work enhances understanding of CRESS-DNA virus evolution and aids in classifying newly discovered viruses.