PS_protein_database

We constructed a comprehensive local database by integrating the NCBI-Nr database (downloaded Aug 10, 2021) with study-specific gene sets (Supplementary Data 1). Phylogenetic species (PS) levels were defined based on the NCBI Taxonomy, with relationships verified or reconstructed phylogenetically. Genes from the target genome were then progressively assigned to these PS levels using Diamond BLASTP (E-value < 1e-3), following a stepwise alignment strategy from broad (cellular organisms) to specific (species-level). For any inquiries, please do not hesitate to contact the corresponding author ([e-mail]).