title: Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.
abstract: Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Pierre-Marc
authors.initials: PM
authors.lastname: Delaux
authors.affiliation: Center for Genomics and Systems Biology, New York University, New York, New York, United States of America.
authors.forename: Kranthi
authors.initials: K
authors.lastname: Varala
authors.affiliation: Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Center for Genomics and Systems Biology, New York University, New York, New York, United States of America.
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
authors.affiliation: Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Ané
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000382:microbiology; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D023281:Genomics; D038821:Mycorrhizae / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny; D013559:Symbiosis / Q000235:genetics*