Internships - Training at the Genomics Student Lab
A different way of doing your internship
As an example below is the GSL project for the academic year 2024/2025.
The topic of the GSL 2025/2026 likely is: Discovery of new viruses in seaweeds.
Genomics Student Lab 3.0 Bachelor Project 2025:
Discovery and Characterization of new RNA Viruses
Background
As far as we know, all living organisms must battle infections from or more virus species. As such, viruses play a crucial role in life on earth. However, while human pathogenic viruses receive considerable attention, other viruses, including phytoviruses, remain underrepresented in life sciences research. This is partly due to the long-standing paradigm that viruses, being non-living entities, do not belong in the "tree of life." Yet, given their profound influence on living organisms, understanding their biology is essential. A critical step in this understanding is the identification and characterization of as many viruses as possible from the global virome. Fortunately, advancements in high-throughput sequencing technologies have greatly enhanced our ability to detect viruses in diverse organisms.
Mostly, viruses are studied in the context of disease. However, RNA viruses also offer unique insights into RNA functionality. RNA is an extraordinarily versatile molecule, performing a wide range of cellular functions. Despite decades of research uncovering its many roles, new RNA functionalities and continue to emerge. Since RNA viruses rely on RNA as their genetic material, studying them can reveal novel aspects of RNA biology.
One fascinating aspect of plant-virus interactions is the plant’s ability to fight infections using small-RNA-based defenses. These small-RNA “antibodies” can recognize and destroy viral RNA genomes. Viruses, in turn, exhibit an extraordinary array of strategies to invade their hosts and propagate. Their rapid mutation rates, coupled with natural selection, enable swift adaptation to host environments, often utilizing previously unknown RNA functionalities.
There is a saying: “Anything you can think of happening to RNA, there is a [plant] virus somewhere doing exactly that”. We believe that it should be expanded to include: “… and many things you would never think of.”
The challenge, then, is to identify RNA viruses with novel characteristics that may uncover unknown RNA functions. To maximize our chances of such discoveries, we turned to a particular environment that could serve as a breeding ground for undiscovered phytoviruses: the (urban) botanic garden. These gardens represent green "islands" where plants have been maintained in relative seclusion for generations, often growing in close proximity to exotic plant species from around the world. This unique setting presents an excellent opportunity to discover new or variant RNA viruses in plants.
By leveraging cutting-edge sequencing and analytical methods, this project aims to expand our understanding of plant viruses, their adaptations, and our knowledge of RNA biology.
References
- Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D; RNA Virus Discovery Consortium; Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 2022;185(21):4023-4037.
- Scholthof HB, Scholthof KBG. Plant virology: an RNA treasure trove. Trends Plant Sci. 2023 Nov;28(11):1277-1289.
- Dekker RJ, de Leeuw WC, van Olst M, Ensink WA, van Leeuwen S, Breit TM, Jonker MJ. A A new Polerovirus species in plants from the Asparagaceae family defined by its RNA-silencing repressor protein P0. bioRxiv. 2024; doi.org/10.1101/2024.09.10.608920.
- Dekker RJ, de Leeuw WC, van Olst M, Ensink WA, van Leeuwen S, Breit TM, Jonker MJ. A new Betaflexivirus species in Ferraria crispa plants. bioRxiv. 2024; doi.org/10.1101/2024.09.02.610804.
- Vaucheret H, Voinnet O. The plant siRNA landscape. Plant Cell. 2024;36(2):246-75.
- Dekker RJ, Rauwerda H, de Leeuw WC, van Olst M, Ensink WA, van Leeuwen S, Meijs C*, Baksi MMM*, Breit TM, Jonker MJ. Discovery of new and variant Potyviruses in Asparagales plants from a Dutch urban botanic garden. bioRxiv 2024.10.09.617369; https://doi.org/10.1101/2024.10.09.617369 *Bachelor project students
- Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A. 2010;107(4):1606-11.
- Jones RAC. Global Plant Virus Disease Pandemics and Epidemics. Plants (Basel). 2021;10(2):233.
Research question
What new or variant RNA viruses are infecting plants from a Dutch urban botanic garden?
Methods and techniques
Plant samples from the Hortus Botanicus Leiden will be analyzed. The research process includes:
- RNA extraction: Isolating and quantifying small-RNA (sRNA) and mRNA.
- Library preparation: Constructing and quality controlling sRNA-seq and mRNA-seq libraries.
- Bioinformatics analysis: Using computational tools to identify and characterize viruses and virus-related host defense responses.
- Molecular-biology techniques: Completing partial viral sequences using mol. biol. methods.
- Detection: Determining the distribution of discovered viruses across all samples using qPCR.
Overall planning*
Week 1: Introduction, background, literature, start writing introduction
Week 2: RNA isolation and quantification, small-RNA & mRNA
Week 3: Sequencing library preparation, sRNA-seq & mRNA-seq
Week 4: Sequencing library preparation sRNA-seq & mRNA-seq
Week 5: Start RNA sequencing data analysis
Week 6: RNA sequencing data analysis and interpretation
Week 7: RNA sequencing data analysis and interpretation
Week 8: RNA sequencing data analysis and interpretation
Week 9: PCR & RACE analysis
Week 10: PCR & RACE analysis
Week 11: Start writing report
Week 12: Writing report & preparation presentation
Week 13: Writing report & preparation presentation
* Subject to change depending on the findings
For more information contact t.m.breit [at] uva.nl