Research Project 5

Investigation of allele-specific expression in stress-challenged polyploid potato plants using long read transcriptomics

About the Project

National Institute of Biology

Ljubljana, Slovenia

Nadja Nolte

Early Stage Researcher

Marko Petek

Main Supervisor

Kristina Gruden

Co-Supervisor

Mednarodna Podiplomska Sola Jožefa Stefana

PhD enrolment

Research Objectives

Allele-specific expression (ASE) and expression of gene families contribute to phenotypic variation and complex traits. This is difficult to study in tetraploid genomes due to multiple highly similar transcripts. Our objectives are:

  • Benchmark existing methods for allele and gene family transcript  identification in polyploid species using short and long reads data.
  • Develop an integrated pipeline for the analysis of allele-specific expression polyploid species both for Pacbio and Nanopore.
  • Analyze changes in allele expression on tetraploid potato subjected to different environmental stresses.

Envisioned Secondments

  • University of Florida (Lauren McIntyre): Learn statistical methods for allele-specific expression.
  • Biobam (Stefan Goetz): Functional annotation and interpretation of allele-specific lrRNA-seq potato data.

Early Stage Researcher

Nadja Nolte

National Institute of Biology,
Slovenia

 

I am passionate about using bioinformatics, particularly RNA-seq analysis, in plant science.

I hold a Bachelor’s degree in Integrated Life Sciences from Friedrich Alexander University in Erlangen, Germany, and I completed my Master’s in Plant Biotechnology at Wageningen University in the Netherlands in 2022.

My previous research mainly focused on studying gene expression using RNA sequencing. It began during my undergraduate when I analyzed RNA-seq data to study how potatoes respond to heat stress. For my Master’s thesis, I looked at single-cell RNA-seq data from plant roots.

During my Master’s internship at the European Bioinformatics Institute (EBI), I contributed to develop pipelines for the Single Cell Expression Atlas. I continued working at EBI for a year, where I integrated an analysis method into the Expression Atlas.

I was drawn to LongTREC because of its dedication to advancing long-read RNA-seq technology and the opportunity to collaborate and build an international network. As a Doctoral Candidate at LongTREC, my goal is to advance long-read RNA-seq in plant science. Specifically, I aim to develop a pipeline for studying allele-specific gene expression in polyploid plants using long-read RNA sequencing.



About the Main Supervisor and Host Group

Marko Petek

National Institute of Biology,
Slovenia

The host group is composed of a highly multidisciplinary and motivated group of biologists, microbiologists, biotechnologists, mathematicians, engineers, and bioinformaticians. The candidate will have access to excellent equipment and facilities as well as training in soft skills required for reaching research independence.