Project (Jan de Vries)
Comparative genomics and early plant evolution

(1) Co-Expression Analyses in the closest algal relatives of land plants

PI in Göttingen: Jan de Vries
Land plants evolved from streptophyte algae in a singular evolutionary event. Meticulous phylogenomic analyses have now consistently recovered the Zygnematophyceae as the closest algal sister lineage to land plants. Recently, and in close succession, four genomes of representative species from the Zygnematophyceae (three of those are Zygnematophycidae) have become available. While this is a significant advance, our exploration of the functional gene space in these genomes is, for now, limited to mere homology. In this project, we will make use of the robust phylogenetic framework that has solicited the Zygnematophyceae as the closest algal relatives to land plants and the recent surge in genome data for these organisms in a co-expression network approach to understand the origin of functional modules. Co-expression networks allow us to use the homology-based inferences as beacons for a guilt-by-association approach to explore gene neighborhoods for linking homology-based knowns with unknowns. We will generate the required transcriptome data to construct such networks. Building on and comparisons to functional modules established in land plant model systems, we will dissect these networks for predicted hallmark functions of land plants. Our data will establish a framework for studying the deep evolutionary roots of key plant function. In a meta-analysis, we will test the hypothesis that co-expression (edges) of orthologous genes (nodes) strings together a minimal framework for these key plant functions putatively shared by (i) Zygnematophyceae and established in (ii) land plants. From this minimal framework, the concerted action of genes underpinning defining plant functions of the last common ancestor of land plants evolved.

(2) Cymbiomics: multipartite interactions and a large-scale approach to pinpointing symbiotic competence of cyanobacteria

PIs in Göttingen: Sophie de Vries, Jan de Vries, Maike Lorenz
The symbiotic interaction between cyanobacteria and eukaryotic hosts had a profound impact on the evolution of life on this planet. It was a cyanobacterial symbiont that eventually was turned into chloroplasts for carbon-fixation. Yet, there is another type of cyanobacterial symbiosis for nitrogen-fixation, and the one where cyanobionts are tightly integrated into the host body but have not (yet) been domesticated into an organelle. Such interactions are best-described in the plants Gunnera, Azolla, cycads, mosses, liverworts and the hornworts, but also the fungus Geosiphon. The manifold occurrence of symbiotic cyanobacteria, many of which are still capable of living together and apart from their host, warrants the question what made them eligible for a symbiosis in the first place. This project tackles the question on What manifests the symbiotic competence of these cyanobacterial lineages?

We will leverage the SAG collection in Göttingen and sequence the genomes of symbiotic and non-symbiotic cyanobacterial strains. We will phenotype cyanobacterial symbiotic competency using the model hornwort system Anthoceros. The genomic and phenotypic data will be combined for genome-wide association studies and comparative genomics. From this factors linked to the symbiotic capabilities of the cyanobacteria will be determined.

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Delaux P-M, Hetherington AJ, Coudert Y, Delwiche C, Dolan L, Dunand C, Gould S, Kenrick P, Li F-W, Philippe H, Rensing SA, Rich M, Strullu-Derrien C, de Vries J. Reconstructing trait evolution: A guideline for plant evo-devo studies (and beyond). Curr Biol in press

de Vries J, Curtis BA, Gould SB, Archibald JM: Embryophyte stress signaling evolved in the algal progenitors of land plants. Proc Natl Acad Sci USA 115: E3471-E3480. (2018)

Nishiyama T, et al. The Chara genome: secondary complexity and implications for plant terrestrialization. Cell 174: 448–464. (2018)

de Vries J, Archibald JM: Plant evolution: landmarks on the path to terrestrial life. New Phytol 217: 1428–1434. (2018)

de Vries J, de Vries S, Slamovits CH, Rose LE, Archibald JM: How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant Cell Physiol 58: 934-945. (2017)

Streptophyte phylogeny and the origin of land plants. We use systems biology to compare land plants to their closest relatives (orange) to infer the molecular biology of their shared ancestor (circular inset).
modified from de Vries & Archibald (New Phytologist [2018] 217: 1428-1434)