This repository contains a jupyter notebook with the code used for comparison of the orthologous gene sets between different organisms. The analysis was developed for and used in this paper:
Dziuba M.V., Müller F.D., Pósfai M., Schüler D. (2023) Exploring the host range for genetic transfer of magnetic organelle biosynthesis. In preparation.
The script accepts the pangenome matrix produced by get_homologues software as input and retrieves the orthologous gene sets shared by a specified organism or a group of organisms in comparison to the other groups. In additions to the lists of such genes, it produces Venn diagrams for visualization of the orthologous groups destribution.
Magnetosomes produced by magnetotactic bacteria have great potential for application in biotechnology and medicine due to their unique physicochemical properties and high biocompatibility. Recent studies uncovered the genetic determinants for magnetosome formation and inspired ideas to transfer the pathway into hitherto non-magnetic organisms. However, previous efforts to genetically magnetize other species have been successful in only a few bacterial recipients, revealing significant challenges in this strategy. Here, by systematic examination of 25 proteobacterial hosts, we generated 7 novel magnetosome-producing strains. To find out, which accessory genes might support magnetosome formation, we compared the orthologues genes found in the genomes of all of the magnetized strains vs. the strains failed to produce magnetosomes in our experiments.
The pangenome matrix produced by get_homologues with the following parameters for defining clusters of orthologous proteins: OrthoMCL clustering algorithm, the cut-off threshold for pairwise blastp alignments E value < 10e-5 and a minimal protein coverage of 50%.
The cleaned (tidy) pangenome matrix with proper species names and containing only the species selected for the analysis:
The collection of all found orthologous protein clusters can be found here: