Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

摘要

Scheme summarizing the steps of the methodology. In order to determine the catalog of genes related to LPG synthesis, searches were performed in three databases (primary literature (NCBI/PubMed; Google Scholar) and metabolic information (KEGG)). To establish orthology relationships, the nucleotide and amino acid sequences of these genes were obtained from TriTrypDB along with 22 genomes and proteomes of trypanosomatid species. To evaluate the similarity between these sequences, three variants of the BLAST algorithm were used, and the execution of these sequences was performed using a custom-tailored Python script and subsequently curated, yielding groups of ortholog genes across species. The phylogenetic reconstruction was performed from the alignment of the groups using Muscle, and the evaluation of phylogenetic signal in the groups was performed with Tree-Puzzle. The most informative evolutionary model was estimated with jModelTest2 and a maximum likelihood phylogenetic tree was constructed using PHYML