The HYPervariability of HYP effectors in potato cyst nematodes

This story is now available as a preprint on bioRxiv and can be read here. If you have comments, suggestions or would like to discuss this with me, please feel free to reach out to me via email or other social media.
Plants use a large arsenal of proteins to recognize and prevent pathogens from causing diseases. Any successful pathogen thus has to deploy proteins termed ‘effectors’ to suppress the plant’s defense system.
This project focused on a highly unusual effector family of potato cyst nematodes called HYPs. HYP effectors consist of a ‘hyper-variable’ middle domain that displays extreme genomic variability in number and organization of subfamily-specific repeats. This domain is flanked by conserved regions that are 95% identical between species and have remained unchanged for ~30 million years. In other words, the repeats in the middle region of the gene are ‘shuffled’ in number and how they are organized while keeping the neighbouring regions conserved. How a genome can permit such a large variation in these genes while still maintaining identity in the conserved regions cannot be explained using currently known genetic mechanisms.
I used long-read sequencing technologies such as Oxford Nanopore and PacBio-HiFi to unravel the underlying genetics of these distinct genes.