Evolutionary History Of The Angiosperm Npf1 Gene Subfamily: Duplications, Retention And Functional Implications For Root Symbioses And Development

The success of land plants can be attributed to the evolution of beneficial associations between plant roots and soil microbes. Root-microbe mutualisms extend the range of plant nutrient acquisition delivered through the hyphal network of mycorrhiza, an ancient and widespread plant symbiosis, or by the more recent adaptive innovation of nitrogen-fixing nodule symbioses. A plant’s genetic toolkit governs its selection of beneficial symbionts and the developmental extent of these intimate interactions. However, the evolutionary origins and function for only a few symbiotic signaling components have been explored. The central aim of this dissertation is to resolve the evolutionary events that contributed two, novel genetic components for establishing root symbioses, NPF1B and NPF1C. The Medicago truncatula (Mt) LATD/NIP/NPF1.7C transporter functions in root and nodule meristems and is a member of the large NPF1 gene subfamily. Here, I propose that LATD/NIP’s role in establishing nitrogen-fixing symbioses is derived from the ancient mycorrhizal signaling pathway. I used a comparative phylogenomic approach to investigate the evolutionary origins of the NPF1 gene across flowering plants and then asked whether diversifying or purifying selection forces influenced NPF1 gene retention. I postulated that such gene retention correlates with the adaptive traits of mycorrhizal or nitrogen-fixing root nodule symbiosis; to test this I measured trait correlation within my dataset. I found that the NPF1 phylogeny is comprised of five well-supported angiosperm clades, A, B, C, D1 and D2, that arose by successive duplications and have unequal gene retention. NPF1B is present as a single copy gene or lost entirely, while the other major NPF1 clades expanded to multiple genes within angiosperms. The NPF1A, B and C genes are under strong purifying selection while the NPF1D genes display positive, diversifying selection. My data revealed a statistically significant correlation of NPF1A, B, C, and D2, but not NPF1D1, gene retention with the ability of a species to form mycorrhizal associations. Additionally, the retention of the NPF1B, C, D1, D2, but not NPF1A, genes within a species is statistically correlated with its ability to form nitrogen-fixing symbiosis. Supporting this correlation, NPF1B genes are expressed in plant root tissues with and without mycorrhizal fungi yet available datasets failed to detect NPF1B expression in nodule tissues whereas the NPF1C genes are expressed in both symbiotic and nonsymbiotic plant root tissues. In support of functional conservation, expression of legume LATD/NIP cDNAs from Cicer arietinum (Ca) and Lotus japonicus (Lj) restored, in part, the root and nodule defects of the Mtlatd mutant and resulted in the formation of peculiar hybrid lateral root-nodule structures while, in wild-type M. truncatula, significantly augmented root development. In L. japonicus, the disruption of LATD/NIP alters the number of lateral roots and nodules My thesis data support the hypothesis for an ancestral NPF1 gene function in establishing mycorrhizal associations in angiosperms and, consequent to the monocoteudicot divergence, co-opted this function for accommodating nitrogen-fixing symbioses in eudicots. Successive duplications then yielded the NPF1B and NPF1C genes that, by neofunctionalization and natural selection, further refined their roles in root organogenesis and symbiosis; a prerequisite for the evolution of nodule organs.