Brown Lab Plant Ecology & Genomics

Research

From whole floras to single cells

We use field experiments, large comparative datasets and new genome-scale software to understand how plant genomes, and the plants that carry them, evolve.

01
PhD project · 2025–2028

Somatic mutation variation in plants

Plants have no segregated germline: a mutation arising in a growing shoot can be passed on through the flowers that shoot eventually bears. Yet compared with animals, remarkably little is known about how often somatic mutations occur in plants or what governs their rate.

With Alex Cagan (University of Cambridge) and the Wellcome Sanger Institute, we are measuring somatic mutation rates in long-lived versus short-lived plant species, and benchmarking sequencing technologies for how reliably they call low-frequency variants. This work is supported by a Cambridge Philosophical Society Sedgwick PhD studentship.

FundingSedgwick PhD studentship, Cambridge Philosophical Society (2025–2028)
PartnersUniversity of Cambridge · Wellcome Sanger Institute
02
Genome structure

Plant organelle genomes

Plant mitochondrial genomes are among the strangest in biology: they recombine across repeats, exist as multiple alternative structures within one cell, and vary more than a hundred-fold in size. That makes them notoriously hard to assemble, and fascinating to compare.

Building on tools developed at the Sanger Institute (gfatk and Oatk), we are assembling mitochondrial genomes across a phylogenetically diverse sample of plants to ask how structure and gene order (synteny) evolve. Our preprint with collaborators at EMBL-EBI and the Darwin Tree of Life builds a pangenome spanning over 300 land plant mitochondrial genomes: gene content is highly conserved, but synteny collapses almost entirely in vascular plants, and genome size and repeat content are the strongest predictors of structural complexity.

PaperOatk, Genome Biology, 2025 Softwaregfatk: organelle assembly graphs Interactive figureMitochondrial assembly complexity across land plants
TalkStructure and synteny across diverse plant mitochondrial genomes. PopGroup 2026, Lille
PreprintConserved genes, discordant structure, bioRxiv, 2026
03
Comparative genomics

Telomeres across the tree of life

Telomeres cap the ends of linear chromosomes with short tandem repeats: TTAGGG in vertebrates, TTTAGGG in most plants. But as reference genomes multiply, it is clear that canonical repeats vary far more than once thought, with some lineages having switched sequence entirely.

We developed the telomere identification toolkit (tidk) to discover and map these repeats rapidly, and are now applying it across the Darwin Tree of Life genomes to chart where and how often telomere sequences have changed.

Papertidk, Bioinformatics, 2025 Softwaretolkit/telomeric-identifier · ★180
04
Polyploid genomics

Auto- or allopolyploid?

Polyploids are traditionally split into two kinds: autopolyploids, which duplicate a single genome, and allopolyploids, which combine the genomes of two species. In reality many polyploids sit somewhere in between, and the label says little about how diverged their chromosome copies actually are.

We are developing ploidyspec to measure this directly. Given haplotype-resolved assemblies of a single individual, it uses k-mer distances to quantify how diverged each chromosome's copies are, searches for retained ancestral chromosome pairs, and estimates a continuous auto–allo index from fossil transposable-element k-mers that distinguish subgenomes. No reference genome or alignment is needed.

SoftwareARU-life-sciences/ploidyspec ReviewThe emerging importance of cross-ploidy hybridisation, Mol. Ecol., 2024