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

Marko Petek

Main Supervisor

Kristina Gruden


Mednarodna Podiplomska Sola Jožefa Stefana

PhD enrolment

Yearly salary

25.453,20 € (Gross)

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.

About the Main Supervisor and Host Group

Marko Petek

National Institute of Biology,

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.