Julie Boisard, PhD
Department of Cell and Molecular Biology Molecular Evolution Uppsala University, Sweden
Genome Architecture in Early-Diverging Eukaryotes
How does genome structure evolve across the eukaryotic tree of life?
About
I am an evolutionary genomicist studying genome architecture in early-diverging eukaryotes.
My research integrates long-read genomics, comparative analysis, and bioinformatic tool development to examine how structural genome features evolve beyond gene inventories.
By focusing on undersampled protist lineages, my work expands phylogenetic representation and helps refine models of eukaryotic genome evolution.
Research Overview
1. Genome Architecture and Structural Evolution
Protein-coding genes represent only one layer of genome evolution, while large fractions of eukaryotic genomes consist of repetitive elements, non-coding regions, and structural features whose evolutionary dynamics remain poorly characterised in early-diverging lineages.
I am interested in how these structural components:
- vary across related species
- reshape genome organisation
- interact with processes such as rearrangement and transposable element activity
My work examines genome architecture as an evolutionary dimension that may follow trajectories partially independent from gene repertoire change.
2. Bioinformatic Tool Development for Comparative Genomics
Studying genome architecture in divergent eukaryotes requires methodological innovation.
I develop and implement reproducible bioinformatic frameworks to support:
- structural genome annotation
- repeat landscape analysis
- integrative evidence scoring
- phylogenetically informed comparative analyses
Tool development in my research is driven by biological questions and improves analytical resolution in phylogenetically divergent, non-model systems.
3. Protist Biodiversity and Deep Eukaryotic Lineages
Protists represent the majority of eukaryotic diversity yet remain underrepresented in genomic databases.
Through the generation and analysis of high-contiguity genome assemblies from undersampled taxa, my research improves phylogenetic representation and documents structural genome variation among understudied eukaryotic lineages.
These data provide comparative frameworks for reconstructing early eukaryotic genome evolution.
Technical Expertise
- Long-read genome sequencing and assembly (Oxford Nanopore)
- Structural genome annotation and repeat analysis
- Gene model prediction and functional annotation
- Comparative genomics
- Phylogenetic reconstruction
- Reproducible computational workflows
- Protist culturing and genomic sample preparation
Selected Publications
Boisard, J., Williams, S.K., Roger, A.J., & Stairs, C.W. (2026). CoMR: an integrative scoring pipeline for comprehensive mitochondrial proteome reconstruction across eukaryotes. bioRxiv. https://doi.org/10.1101/2026.02.20.707009
(Integrative bioinformatic framework for mitochondrial proteome reconstruction in model and non-model eukaryotes.)
Aguilera-Campos, K.I., Boisard, J. et al. (2025). Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function. The ISME Journal 19(1): wraf171. https://doi.org/10.1093/ismejo/wraf171
(Metagenomic characterisation of prokaryotic partners associated with anaerobic breviates.)
Boisard, J. et al. (2022). Marine gregarine genomes reveal the breadth of apicomplexan diversity with a partially conserved glideosome machinery. BMC Genomics 23:485. https://doi.org/10.1186/s12864-022-08700-8
(Comparative genomics and structural diversification in divergent apicomplexans.)
Boisard, J. & Florent, I. (2020). Why the -omic future of Apicomplexa should include gregarines. Biology of the Cell 112:173–185. https://doi.org/10.1111/boc.202000006
(Conceptual perspective on expanding genomic sampling in apicomplexan protists.)