The dynamics of intra-species gene birth in the nematode Pristionchus pacificus

Advisor: Christian Rödelsperger

Location: Max Planck Institute for Biology

Nematodes are one of the most successful animal phyla that have colonized virtually all ecological niches. It has been hypothesized that the adaptation to new environments is facilitated by the emergence of novel genes, which may explain the high number of lineage-specific genes in certain clades. For example, one third of all genes in the beetle- associated Pristionchus pacificus have no detectable homologs in Caenorhabditis elegans or any other species outside the family Diplogastridae, which suggests that these genes evolved recently in the lineage leading to P. pacificus. Over the past years, genetic studies in P. pacificus demonstrated that such genes control important developmental decisions and novel behaviors. Through complementary genomic studies we have extensively characterized the evolutionary dynamics of these novel genes. These analyses supported a model where the highest rates of gene birth will occur at the intra-species level. To study this evolutionary process, we plan to compare transcription and translation between closely related strains of the same species. Our laboratory has already generated high quality genome assemblies for several P. pacificus strains that were annotated using RNA-seq data. Dr. Catia Igreja, a group leader in our Department, has established a protocol for ribosome profiling (Ribo-seq), a method to measure active translation of protein-coding genes^.

Model of intra-species gene gain and loss. Our preliminary data supports that there are many more transcriptionally active regions in the genome than the actual number of protein-coding genes. Most of these sequences evolve effectively neutral and will be lost over longer evolutionary periods. However, throughout the lifetime of such sequences, point mutations and indels can change their coding status thus giving rise to the formation of novel proteins

Model of intra-species gene gain and loss. Our preliminary data supports that there are many more transcriptionally active regions in the genome than the actual number of protein-coding genes. Most of these sequences evolve effectively neutral and will be lost over longer evolutionary periods. However, throughout the lifetime of such sequences, point mutations and indels can change their coding status thus giving rise to the formation of novel proteins

Project goal:
This project combines experimental and computational work with the main goal to explore transitions between protein-coding genes, non-coding genes, and inactive genomic regions in different strains of P. pacificus. To this end, the student will need to learn the ribosome profiling protocol and apply it for several P. pacificus strains and other species. In the meantime, I will train the candidate in the application of all bioinformatic tools that will be required for the analysis of genomic, RNA-seq and Ribo-seq data. The combined analysis of genomic, transcriptional, and translational data will ultimately allow us to quantify which mechanisms (gain of transcription and translation, ORF switching, indels and structural variations) predominantly contribute to the emergence of novel genes in P. pacificus.

More information about the research of Christian Rödelsperger and a selection of recent publications can be found on his faculty page.

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Application deadline: 27 January 2025