UACG

UACG reconstructs archaeal phylogenomic trees by concatenating a curated set of 128 single-copy core genes to infer evolutionary relationships within the Archaea.

Key Features:

• Extension of UBCG framework: Extends the up-to-date bacterial core gene (UBCG) framework to archaeal phylogenomics.
• Core gene set: Uses a curated set of 128 single-copy core genes optimized for resolving archaeal phylogenies.
• Concatenation-based phylogenomics: Employs a concatenation approach combining core gene sequences into a supermatrix for tree reconstruction.
• Validation on Haloarcula: Applied to the Haloarcula genus and produced phylogenies consistent with orthoANIu dendrograms.
• Comparison with 16S rRNA: Provides a more stable framework than single-gene 16S rRNA-based phylogenies that can be affected by intragenomic heterogeneity.

Scientific Applications:

• Phylogenetic reconstruction: Infers evolutionary relationships among archaeal species using multi-gene concatenated data.
• Species delineation: Supports species-level discrimination by providing genome-wide phylogenetic context complementary to methods like orthoANIu.
• Comparative genomics: Enables comparison of gene conservation and divergence across archaeal genomes.
• Evolutionary and adaptation studies: Facilitates exploration of evolutionary patterns and the genetic basis of adaptation within archaea.

Methodology:

Selection of 128 single-copy core genes and concatenation of their sequences into a supermatrix for phylogenetic analysis.