Search for: All records

Abstract Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association. 

Summary Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in fourMedicago truncatula Tnt1‐insertion mutants affected in arbuscular mycorrhizal colonisation. We located theirTnt1insertions and identified alleles for two genes known to be involved in mycorrhization,RAM1andKIN3. We compared the effects of thekin3‐2andram1‐4mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting thatRAM1acts upstream ofKIN3.Additionally,KIN3appears to be involved in the suppression of plant defences in response to the fungal symbiont.KIN3is located on the endoplasmic reticulum of arbuscule‐containing cortical cells, andkin3‐2mutants plants hosted significantly fewer arbuscules than the wild type.KIN3plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild‐type plants, thekin3‐2mutant did not exhibit increased root colonisation under high nitrogen.