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Understanding de novo gene birth (Prof. M. Mar Albà Soler)

The Research Programme on Biomedical Informatics (GRIB, UPF-IMIM) is seeking candidates to apply for a PhD studentship from the INPhINIT "La Caixa" Fellowship Programme. 

The selected candidate will join the Evolutionary Genomics research group of GRIB located at the Barcelona Biomedical Research Park (PRBB).

Project Description

The gain of new genes, or the loss of existing ones, modifies the set of functions that an organism can perform. New genes can appear by gene duplication or by another recently described mechanism, de novo gene evolution. In contrast to duplicated genes, genes evolved de novo from previously non-coding sequences encode protein with completely new sequences. Recently, we have discovered that translation is pervasive and that many transcripts previously believed to be non-coding actually produce small proteins (Ruiz-Orera et al., 2014; Ruiz-Orera et al., 2018). This results in a much larger number of putative de novo gene precursors than previously anticipated.

The impact of de novo gene birth in evolution is still not well-understood. The research to date has mainly focused on annotated protein-coding genes. As a result, our view of the process is very partial and biased towards standard protein-coding genes. In order to fully understand de novo gene birth we will use state of the art sequencing technologies in the model system S.cerevisiae and related yeast species. We will identify recently evolved transcripts in an annotation-independent manner, and determine if the transcripts translate small proteins or peptides using ribosome profiling (Ribo-Seq) and proteomics experiments. With this data in hand we will be able to compare the relative frequency of de novo gene birth and gene duplication events. The study is expected to make an important contribution to the understanding of the evolution of new genes and their functions.

  • Ruiz-Orera, J., Messeguer, X., Subirana, J.A., Albà, M.M. (2014). Long non-coding RNAs as a source of new peptides. Elife 3: e03523.
  • Ruiz-Orera, J., Grau-Verdaguer, P., Villanueva-Cañas, J-L., Messeguer, X., Albà, M.M. (2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution, 2:890-896.

Position Description

Candidates should be highly motivated to do a PhD in the field of Computational Genomics and have an excellent academic record. Basic programming skills and knowledge of R are required for this post. They will use computational tools to quantify the impact of de novo genes in evolutionary innovation. De novo genes can be detected using RNA sequencing (RNA-Seq) techniques coupled with multiple species sequence comparisons.  The PhD candidate will Illumina as well as Nanopore RNA sequencing data to obtain the complete transcriptome. She/he will also identify all translated open reading frames using ribosome profiling data. The number of genes originated de novo will be compared to those originated by gene duplication in the same time interval. The student will also employ different sequence-based methods to measure the impact of natural selection in the emergence and maintenance of new genes.


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