Genomes within genomes: nested symbiosis and its implications for plant evolution

Abstract

Summary Many important plant traits are products of nested symbiosis: mobile genetic elements (MGEs) are nested within microbes, which in turn, are nested within plants. Plant trait variation is therefore not only determined by the plant’s genome, but also by loci within microbes and MGEs. Yet it remains unclear how interactions and coevolution within nested symbiosis impacts the evolution of plant traits. Despite the complexities of nested symbiosis, including nonadditive interactions, understanding the evolution of plant traits is facilitated by combining quantitative genetic and functional genomic approaches that explicitly consider sources of nested genetic variation (from loci in MGEs to microbiomes). Additionally, understanding coevolution within nested symbiosis enables us to design or select for MGEs that promote plant health.

Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont

“…Recent advances in sequencing and microbiome research have revealed the ubiquity of microbial symbioses, meaning that many important host phenotypes, such as plant yield in agriculture or disease-related traits in humans, are actually symbiotic extended phenotypes , their variation being influenced by loci present within interacting microbial symbionts in addition to the host [ 1 – 6 ]. When loci influence fitness-related traits of both host and symbiont, which we henceforth refer to as symbiotic pleiotropy , they determine the degree to which partners' fitnesses are aligned (i.e.…”

Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally-occurring isolates of a model plant symbiont

“…A central goal of genetics research is to build a reliable map of genotype-to-phenotype relationships (G→P map) in order to uncover the genetic basis of important organismal phenotypes, including plant yield in agriculture or disease-related traits in humans (1–3). Recent advances in sequencing and microbiome research have revealed the ubiquity of microbial symbioses, meaning that many of these host phenotypes (yield, disease resistance, et c.) are actually symbiotic extended phenotypes , their variation being influenced by loci present within interacting microbial symbionts in addition to the host (4–9). Studies of the G→P map in single organisms have highlighted the importance of pleiotropy , i.e., loci that influence more than one trait.…”

Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium—Plant Interaction

“…It has been suggested that phenotypic variation should be considered as the sum of environmental variance and of additive and nonadditive contributions. These contributions derive from the genotype of the host and of the mutualistic microbes (including their mobile genetic elements, which largely vary among strains) and from the intergenomic epistasis between hosts and microbes [ 4 ].…”