Datasets for phylogeny-guided analysis of pseudogenes in Pseudomonas aeruginosa

In the study entitled "A large-scale phylogeny-guided analysis of pseudogenes in Pseudomonas aeruginosa bacterium" we analyzed the genomic data of 4699 strains of the bacterium Pseudomonas aeruginosa P. aeruginosa) as they exhibit high variability in the number of annotated pseudogenes.  In particular, we looked for correlations between the number of pseudogenes and other genomic- and meta- features of the strains. We identified orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We mapped and examined orthology relationships between genes and pseudogenes. We generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we dived into clusters of orthologues genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, misannotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future.

We provide the following files:

protein_seq.zip: A fasta file containing 28,948,105 protein sequences of coding genes across all strains.

pseudo_seq.zip: A fasta file containing 86,273 DNA sequences of pseudogenes across all strains. 

protein_clustering_output.zip: Clustering of protein sequences with CD-HIT clustering algorithm and the following parameters: similarity threshold of 70%, word size of 5, and the slow mode version.

pseudo_clustering_output.zip: Clustering of pseudogene sequences with CD-HIT-EST clustering algorithm and the following parameters: similarity threshold of 80\%, word size of 5, and the slow mode version.