Interview: Generating gapless, telomere-to-telomere plant genome assemblies

Caroline Belser works at Genoscope, CEA, in a bioinformatics laboratory where she is involved in several genome projects which aim to produce high-quality genome assemblies using long-read technologies. She is also part of international consortia working on marine biodiversity. We spoke to Caroline about her work using nanopore sequencing to reconstruct large genomes, and the benefit it brings to the study of biodiversity.

In addition to this interview, you can learn more about Caroline’s research, by watching a webinar she recently presented ‘Generating gapless, telomere-to-telomere plant genome assemblies’.

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What are your current research interests?
I’m focusing on eukaryotic genome assemblies, particularly plant genomes.

What first ignited your interest in genetics?
My first internship in molecular biology was with a team working on a genetic disease in children. I then started working at Genoscope during my studies, in the sequencing lab. After eleven years in the sequencing lab, I became passionate about bioinformatics and completed a master's degree in bioinformatics.

How is nanopore sequencing changing the quality of genomic data for the assembly of large genomes? How has it benefitted your work?
The long reads from nanopore sequencing allow us to reconstruct complete genomes with very few gaps. Short-read sequencing technologies provide access to the gene catalogue but don’t allow an estimation of the content in repetitive elements, for example. Very long reads can span very large clusters of genes and very long repetitive elements.

What impact could the construction of more complete and accurate genomes have on the study of biodiversity?
In the example of Musa acuminata (banana), a more complete genome has tremendous value in the research against Fusarium Wilt Disease; in our work, we have been able to reconstruct more copies of the tandemly repeated resistance genes in the Musa acuminata genome. There is also a benefit for evolutionary research in the Musaceae family, and for breeders.

What have been the main challenges in your work and how have you approached them?
The main challenges are to constantly seek to improve methods, and to keep abreast of developments in bioinformatics and new molecular biology methods. This is what makes our job so exciting too.

What’s next for your research?
We want to solve more and more complex genomes, including those with high heterozygosity and polyploidy.