Research Project 4

Long read RNA sequencing to annotate the genomes across the eukaryotic tree of life

About the Project

Centre for Genomic Regulation

Barcelona, Spain

Roderic Guigó

Main Supervisor

Universitat Pompeu Fabra

PhD enrolment

Yearly salary

29.959,57 € (Gross)

Research Objectives

lrRNA-seq will become essential for gene annotation in the Earth Biome Project. Challenges exist to capture the transcriptome comprehensively (for long or rare transcripts and from multiple tissues) and to map transcripts across species. Our objectives are:
  • Develop methods to efficiently map lrRNA-seq reads across species.
  • Develop methods to normalize lrRNA-seq libraries and/or to target low abundant transcripts.
  • Develop methods for targeting and sequencing very long RNA molecules.

Envisioned Secondments

  • Wobble Genomics (Richard Kuo): Learn company’s library normalization methods for lrRNA-se.
  • SU (Kristoffer Sahlin): Assess SU’s mapping algorithms for long transcripts and across-species mapping.

About the Main Supervisor and Host Group

Roderic Guigó

Centre for Genomic Regulation,

The overarching theme of the research in Roderic Guigo’s lab at CRG is the understanding of the information encoding in genomic sequences, and how this information is processed in the pathway leading from DNA to protein sequences. More specifically, we are interested in the epigenetic regulation of gene expression and RNA processing, the relationship between molecular phenotypes and higher order endophenotypes and organismal phenotypes, and the identification of functional regions on the genome of all living beings. Our group is mostly computational, and we do both large-scale data analysis and development of methods, but it has also an important experimental component. We have participated and participate in many large scale international functional genomics projects, such as ENCODE, GTEx, BluePrint and others.