Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects.

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Genome sequencing costs are decreasing, but strategic prioritization is still essential for large-scale projects.
• Identifying organisms with novel genomes maximizes the scientific return on investment.
• Existing selection methods may be biased by previously sequenced organisms.

Purpose of the Study:

• To develop a computationally simple and broadly applicable method for selecting genome sequencing targets.
• To create a phylogenetic scoring system that is independent of previously sequenced datasets.
• To demonstrate the practical application of this method in real-world sequencing initiatives.

Main Methods:

• Inferred a phylogenetic scoring system based on evolutionary relationships.
• Applied pre- and post-processing steps for data refinement.
• Utilized two case studies: the Genomic Encyclopedia of Bacteria and Archaea and the Roseobacter clade phylogenomics.

Main Results:

• The developed method provides a robust approach for selecting phylogenetically diverse organisms for sequencing.
• The method was successfully applied to large-scale (1,000 type strains) and smaller-scale projects.
• Demonstrated the utility and ease of application of the phylogenetic scoring system.

Conclusions:

• The proposed phylogeny-based method offers an effective strategy for prioritizing genome sequencing targets.
• This approach ensures the selection of evolutionarily distinct organisms, enhancing genomic diversity.
• The method is computationally efficient and practical for diverse large-scale sequencing endeavors.