Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens.

摘要: Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns associations with their hosts and factors driving spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected be rampant throughout evolution, which justified use single-locus phylogenies macroevolutionary studies these photoautotrophic bacteria. Genomic approaches have greatly increased amount molecular data available, but selection orthologous, congruent genes that more likely reflect bacterial histories remains problematic. In this study, we developed synteny-based approach searched Collinear Orthologous Regions (COR), under assumption present same order orientation across wide monophyletic clade less undergone HGT. We sixteen reference Nostocales genomes identified 99 genes, part 28 COR comprising three eight each. then bioinformatic pipeline, designed minimize inter-genome contamination processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset 90 representing 25 COR, were used infer phylogenetic relationships within among lichenized Cyanobacteria. was narrowed down further 71 22 by selecting only one (largest) operon per COR. found relatively high level congruence trees derived from 90-gene dataset, slightly higher compared However, topological significantly resulting concatenation species tree based on 90- 71-gene datasets highly congruent, most supported result obtained when using synteny, collinearity, information (i.e., dataset) as gene criteria, outperformed larger genes.