Project properties
Title Elucidating the evolution of symbiosis genes across plant genomes
Group Biosystematics Group
Project type thesis
Credits 24-36
Supervisor(s) Dr. Robin van Velzen
Examiner(s) Dr. Freek Bakker, Prof. dr. M.E. Schranz
Contact info Robin.vanvelzen@wur.nl
Begin date 2022/10/30
End date 2025/12/31
Description Description Nitrogen is a critical limiting element for plant growth. Some plants, make specialized root organs called nodules where they intracellularly host nitrogen-fixing bacteria. The most well-known are legumes, but some relatively distantly related plant groups can also have the ability make symbiotic root nodules. Traditionally, nodulation was considered to represent a case of many independent gains of this symbiotic trait. Recently, however, phylogenomic studies revealed that genes that function in establishing or maintaining nitrogen-fixing nodules (NIN, RPG and NFP2) are independently lost in non-nodulating relatives of nitrogen-fixing plants. This supports a scenario of a single gain followed by massively parallel loss of nitrogen- fixing root nodules. However, loss of such symbiosis genes was based on genomic information of relatively few plant lineages. In this project, you will elucidate the evolution of symbiosis genes across a large set of available plant genomes to test the massive parallel loss hypothesis.
Some specific research questions are:
-Are symbiosis genes consistently lost across genomes of non-nodulating plants?
-When were these genes lost and/or pseudogenized?
-What are the geological or climatological factors correlating such massive loss of the root nodule symbiosis?
To address these questions, you will mine symbiosis gene loci across multiple plant genomes based on microsynteny and phylogenetic analyses to identify shared and unique signatures of gene loss and/or pseudogenization. By placing these patterns in the context of plant species relationships, you will assess which ancestral species lost the symbiosis trait and when. This can be correlated with climatic factors such as ancient decreases in atmospheric CO2.


Used skills Bioinformatics, Comparative genomics, Phylogenetics
Requirements starting date to be discussed.