5 Questions to Alice Dennis, chair of the Annotation Committee

Read the full interview with Alice Dennis below:

My name is Alice Dennis and I am a lecturer at the University of Namur in Belgium.

I've been here for about 2 years and I've been working with ERGA for even longer.

I started in the early days, maybe around January, 2021 when it was coming together and I was really interested in this idea of constructing genomes from more diverse taxa. One of my main motivations was that I work on a snail in a group of pulmonates that is very underrepresented in the literature, and so I was trying to help build up enthusiasm for sequencing close relatives and things like this. When I first joined ERGA, I volunteered to start helping the annotation committee with this idea of increasing biodiversity representation and I've been here ever since.

At the annotation committee, we have monthly meetings where everyone is welcome to see our discussions about tools for genome annotation and challenges we are facing. And I really would like to see greater participation across ERGA because this is the step in genome assembly that is often forgotten. So, annotation tools are lagging behind those for assembly. And even more so, we are missing the tools for evaluating our annotations. And so these are the things we're interested in at the annotation committee.

We also have experts from different aspects of annotation who are much more versed than me and things like repeat prediction and gene family evolution and these sorts of very interesting analyses of course. And so everyone is welcome to come to our meetings and see what we're talking about, but I would also like to start making room for people to bring their annotation problems and projects. And so we can create space within all of our meetings or even have larger efforts if people want to approach us to know how their projects are going or to get specific feedback.

Video: Alice presenting the work of the Annotation Committee during the Biodiversity Genomics Conference 2023

So I think that one of the main challenges is that we are still having trouble finding good pipelines. We really highlighted this recently. A group of us went to the BioHackathon in November 2023. Mostly people from the annotation committee at ERGA or people we had found through there, but also researchers from around the world via the biohackathon. And we sat down and we really found some of the hurdles to creating annotation and a lot of this is in gathering the right amounts of evidence, things like RNAseq and protein data. And this is really lacking in a lot of systems. And so I think this sort of resource building is the main challenge. And from my own work in molluscs we see that the lack of close relatives really limits our ability to work with homology based approaches. So we really need to improve our taxonomic representation.

I think the most exciting thing in the coming years is that we're going to have more genomes to compare. And so this is free of technologies, but it is of course enabled by projects like the genome assembly going on in ERGA because having more close relatives will mean that we can improve our annotation and we can have much better predictions of genes and gene features and other structural aspects of genomes. This will be a huge leap forward in annotation.

I really also think this will be improved by having more user friendly tools and these are under development by lots of people. And so I hope we as a committee can help facilitate this and bring to the forefront the best tools for each different taxonomic group, but hopefully to standardize this as much as possible across taxa. And lastly, I think with the long read technologies that are coming out, we are going to have better annotations. And so as these become cheaper and have fewer errors, we can really utilize long reads to improve genome annotation.

I hope in the next months and years we can really try and bring in more of the ERGA community to see how important annotation is. I would like to bring in more recommended packages for people to use if you go to our web page now, there is one or 2 pipelines recommended as well as an overview of the steps and annotation. So I hope we can increase and improve these resources for people and try to make these available to everyone. And like I mentioned, I think the next thing we really want to do is be available for people who would like feedback and help with their annotations.

Everyone is welcome to join our committee and ways to get in touch with us are varied.

We are on KeyBase and we check that regularly. We have a mailing list if you would like to join that and receive reminders of all of our meetings. Or if you would just like more information, you can email (annotation@erga-biodiversity.eu).

And I hope to see you all at our meetings, which are currently on Monday afternoons, just once a month.

Find Alice on Mastodon @AliceDennis@genomic.social

Send an email to the Annotation Committee and learn how you can contribute!