Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

• DOI: 10.1099/mgen.0.000351
• Publication Date: 2020-03-16T17:16:58Z
• Authors: Maria Izabel A. C...; Sara Moeskjær; Camous Moslemi; Bryden Fields; Asger Bachmann; Bjarni J. Vilhjál...; Mikkel Heide Schi...; J. Peter W. Young; Stig U. Andersen
• Keywords: 0301 basic medicine; introgression; rhizobia; Genetic Introgression; CONJUGAL TRANSFER; SEQUENCE; Plant Roots; Linkage Disequilibrium; 03 medical and health sciences; Bacterial Proteins; Selection, Genetic; Symbiosis; Phylogeny; 2. Zero hunger; Rhizobium leguminosarum; 0303 health sciences; MANTEL TEST; Whole Genome Sequencing; High-Throughput Nucleotide Sequencing; SINORHIZOBIUM; EVOLUTION; POPULATION GENOMICS; symbiosis; NODULATING STRAINS; Haplotypes; IV SECRETION SYSTEM; LATERALLY TRANSFERRED GENES; genome assembly; PHASEOLUS-VULGARIS; white clover; Trifolium; conjugation; Research Article; Plasmids

Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196

Rhizobium leguminosarum

sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.