Viruses are central players in microbial communities and viruses also have a major effect on communities of eukaryotic organisms. This interaction has important consequences for the evolution of cellular organisms. We now have the technology to measure the genetic content of communities at high resolution and we can infer which organisms with which detailed genome organization they contain, including all community members - eukaryotes, prokaryotes, and viruses. In my research group, we develop methods for the reconstruction of genomes and their evolutionary histories and gain biological insights by analyzing data with these methods. Specifically, we develop and apply approaches (i) to reconstruct viruses from metagenomic and metatranscriptomic data and (ii) to infer microbial population genetic processes from genomic and metagenomic data.

News

February 2025

• Emma Nabuurs started as a BSc thesis student, she will integrate genomic location into Goldfinder, a tool to estimate gene co-occurrence in microbial pangenomes

November 2024

• Thomas de Bruijn started as a PhD student - in co-supervision with Hilje Doekes from the Laboratory of Genetics, he will work on modelling diversity in bacteriophages. Welcome Thomas!

September 2024

• Laura Patiño Medina started as a PhD student - in co-supervision with Astrid Bryon, she will work on microbiome-virome interactions in whiteflies. Welcome Laura!
• A new Msc student started: Liz Villabona Arenas will work on featurization of plant virus genomes, in co-supervision with Dimitris Karapliafis. Welcome Liz!

July 2024

• We are looking for a PhD student: In this project, you will combine bioinformatics and modelling to untangle the drivers of phage diversity across space and time. Co-supervised by Hilje Doekes from the Laboratory of Genetics
• New paper published: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins If you do not have access, contact me for the pdf or look at the latest biorxiv version.
• Join us for the EMBO lecture course on Evolutionary and Comparative Genomics, abstract deadline: 31 July 2024

May 2024

• We are looking for a PhD student: join us if you want to work on insect virome analysis, togeter with me and Astrid Bryon from the Laboratory of Virology
• A new preprint is out - Goldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes
• Inge van Vugt successfully defended her Msc thesis, congratulations!

April 2024

• The consensus statement from the RdRp summit is published: Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities

January 2024

• Chen Chen started her PhD in co-supervision with Dick de Ridder on deep learning approaches for evolutionary origins of species-specific prokaryotic genes. Welcome Chen!

December 2023

• Laurens Klinkien successfully defended his Msc thesis on protein structure similarities of orphan genes - right before the Christmas party!
• Jun Liu arrived at WUR. After finishing his experiments at CAAS, he will now focus on bioinformatics analyses. Welcome in person, Jun!

November 2023

• Another Msc student started: Inge van Vugt will work on insect microbiomes, with a particular focus to detect RNA viruses, in co-supervision with Astrid Bryon. Welcome Inge!

September 2023

• Felipe Perez Martinez started his Msc thesis on metatranscriptomics of orphan genes in the human gut. Welcome Felipe!

July 2023

• Gian Passania successfully finished his Msc thesis on the detection of endogenous viral elements in Spodoptera species!
• We are looking for a PhD student to join our team - get in touch if you are a bioinformatician who wants to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns
• New preprint is out - Large-scale investigation of orphan genes in the human gut microbiome elucidates their evolutionary origins

May 2023

• A new Msc thesis student started - Laurens Klinkien will work on using protein structures to investigate orphan proteins (in co-supervision with Aalt-Jan van Dijk)
• The conference season is starting. You can find us at BioSB, NLSEB, and ViBiom

April 2023

• Our short perspective on pangenome evolution is accepted in GBE
• Joran Schorlemmer successfully finished his Msc thesis on the surface proteins of phages (in co-supervision with Aalt-Jan van Dijk). Congratulations!

March 2023

• Elma van Wieren successfully finished her Msc thesis on the evolution of auxiliary metabolic genes. Contratulations!
• Devin van Valkengoed sucessfully finished his Msc thesis in co-supervision with Astrid Bryon from the WUR Virology group. Congratulations! We are happy that he stays around a bit longer to wrap up the project.

February 2023

• Nikolai Matviiets sucessfully finished his Msc thesis in co-supervision with Anna Alekseeva from the WUR Genetics group. Congratulations!

January 2023

• Another Msc thesis student started: Gian Passania will work on integrated viral elements
• Dimitris Karapliafis finished his research practice and is ready to start his PhD in the group in February, huge congratulations! Looking forward to explore the evolution of plant viruses!

November 2022

• New paper on phage recombination: Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000915

September 2022

• Three new thesis students are starting: Joran Schoorlemmer, Jori de Leuw, and Elma van Wieren. Welcome!
• New paper published in collaboration with the Virology Goup on Arabidopsis latent virus 1: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18466

August 2022

• Two new thesis students are starting: Devin van Valkengoed and Dimitris Karapliafis. Both will work on virus evolution, welcome!
• Amanda van de Ligt has successfully defended her Msc thesis, congratulation!
• New papper published :) Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids: https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac121/6663764

June 2022

• New paper published :) Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance: https://academic.oup.com/gbe/article/14/7/evac098/6613374

May 2022

• Nikolai Matviiets started his Msc thesis on Meta-omics analysis of fermented milk communities, in co-supervision with Anna Alekseeva from the WUR Genetics group. Welcome Nikolai!

March 2022

• Matthijs Kon has finished his Msc thesis entitled Pipeline comparison for covert virus detection in Spodoptera exigua using high throughput sequencing data. Congratulations Matthijs!

January 2022

• New preprint available: Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids https://www.biorxiv.org/content/10.1101/2022.01.07.475421v1

• Joliese Teunissen started her PhD co-supervised with Stefan Geisen at the WUR Nematology group. She will investigate the microbiome in intercropping. Welcome Joliese!

November 2021

• New preprint available: Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance https://www.biorxiv.org/content/10.1101/2021.11.12.468352v1

• Jan Baijens joined as a PhD student to work on genome evolution of plant viruses. Welcome Jan!

September 2021

• We are looking for a PhD student in deciphering the soil microbiome in intercropping! Forward the announcement to suitable candidates and apply here: https://www.wur.nl/en/vacancy/PhD-Deciphering-the-soil-microbiome-for-optimized-intercropping.htm Feel free to contact me for questions!

• Matthijs Kon has started his Msc thesis on insect virus discovery in sequencing data, in co-supervision with Astrid Bryon. Welcome Matthijs!

• Jun Liu started his PhD project in China co-supervised by Jing He at the Energy Microbiology Center of the Chinese Academy of Agricultural Sciences. Welcome Jun!

August 2021

• We are looking for a PhD student in plant virus genomics! Forward the announcement to suitable candidates and apply here: https://www.academictransfer.com/en/303862/phd-position-virus-diversity-and-evolution-in-natural-plant-ecosystems/ Feel free to contact me for questions!

• The PhD project “Deciphering the soil microbiome for optimized intercropping” is funded by the plant science group at WUR. This will establish a novel a collaboration between Stefan Geisen and me. The project is embedded in a larger consortium of young tenure trackers at WUR. Stay tuned!

July 2021

• The PhD project “Virus diversity and genome evolution in natural plant ecosystems (V-GENE)” has been awarded funding by the graduate school EPS: https://www.graduateschool-eps.info/3-projects-awarded-in-eps-wu-young-tenure-track-call/ Let’s celebrate (now) and look for a candidate (after the holidays)!

• Nikolaos Vakirlis started as a postdoc at Kiel University on a project that I acquired during my time there. We will work in close colaboration. Welcome Nikos!

Contact:

Anne Kupczok
Bioinformatics group
Department of Plant Sciences
Wageningen University & Research
Wageningen, The Netherlands

@annecmg@scholar.social