Comparative Phylogenetic Analysis of Symbiotic Genes of Different Nodule Bacteria Groups Using the Metatrees Method

Abstract

We applied modified phylogenetic analysis method of building meta-trees to study the evolutional patterns of various groups of symbiotic genes (nod-genes control the formation of nodules and nif/fix-genes control symbiotic nitrogen fixation). The method consists in the pairwise comparison of topologies and construction combined dendrograms («meta-trees»), where the relative position of the two trees is a measure of corresponding gene phylogenies congruence. Homologues of 18 symbiotic genes (nodABCDIJN, nifABDEHKN, fixABC, fdxB) are present in each test organism (9 strains belong to the genera Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium and Neorhizobium). These genes were selected for the implementation of this method, as well as the gene 16S rRNA as a traditional taxonomic chromosome marker. We constructed and compared phylogenetic trees for all these genes and then calculated the pairwise similarity coefficients for their topologies. According to the obtained data we built a meta-tree, and there were two statistically distinct gene clusters identified within. Cluster 1 includes mainly nif-and fix-genes and cluster 2-mostly nod-genes, that is related to the data of separate localization of these gene groups in the rhizobial genomes. The exception is the arrangement of nifB and fixC genes with nodA in cluster 2, as well as co-localization of nodI and nifD in cluster 1. During the identified clusters structure analysis we found strong relationship between the relative gene position and the characteristics of their genome localization in nodule bacteria. Importantly, the differences between clusters 1 and 2 are not expressed less clearly than the differences between nod-and nif/fix-gene groups. It is obvious that clusters 1 and 2 of our meta-tree reflect primarily different mechanisms of nodulation evolution and symbiotic nitrogen fixation associated with the independent origin of the relevant gene groups, and possibly, with their separate horizontal transfer between different groups of rhizobia. Further study of the symbiotic gene evolution in nodule bacteria requires improvements used phylogenetic analysis techniques, including separate analysis meta-tree for rhizobia, representing different stages of symbiosis evolution.

Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

“…We observe a clear metatree clustering of genes located together and related to the same (nodulation or N 2 fixation) process. One can assume that the major groups of sym genes (nod, nif/fix) combined mostly independently, although genes that fall into "foreign" clusters revealed on the metatree may indicate their occasional capture during the HGT of the neighbouring cluster or kind of methodological artefacts [63].…”