Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of arbuscular mycorrhizal symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage

Pierre-Marc Delaux

2014

Scholarcy highlights

  • Eukaryotes interact with microbes in a dynamic network of symbiotic associations
  • To investigate the distribution of non-host species across the Brassicales, we tested the symbiotic status of eighteen Brassicaceae species, including Aethionema arabicum that belongs to the earliest diverging lineage in the family, and fourteen other species distributed across more basal Brassicales families, including Cleomaceae, Resedaceae, Limnanthaceae and Moringaceae
  • In order to determine when the ‘symbiosis-specific’ genes have been lost in Brassicales and test if this loss correlates with the loss of the symbiotic ability, we assessed the presence of these genes in five sequenced Brassicaceae genomes, in the transcriptomes of four other Brassicaceae, including Aethionema arabicum, and in thirteen other taxa belonging to more basal Brassicales families
  • We reconstructed the evolutionary history of 33 fully sequenced plant genomes using BigPlant, a phylogenomic pipeline originally developed to analyze genomes and transcriptomes of seed plants. Using this phylogenomic framework to analyze the genomes of 33 fully sequenced species, we identified a set of 395 ortholog groups, corresponding to 305 and 409 genes in Medicago and rice, respectively, that are highly conserved across land plants, but missing in the genomes of the five Brassicaceae sequenced to date
  • The arbuscular mycorrhizal symbiosis and the symbiotic toolkit required for its establishment are highly conserved among land plants
  • Our analysis integrating genomic and transcriptomic data strongly supports that the loss of AM symbiosis repeatedly lead to the loss of an entire set of genes required for this symbiosis
  • To determine the enrichment in symbiosis-related genes of generated lists, each accession number of the list was searched against a list composed by the genes up-regulated in arbuscules and the ‘symbiosis-specific’ genes included in the current Medicago truncatula gene model

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