Highlights

In-depth looks at key studies

A closer read of a few studies from the lab — what the question was, how we approached it, and what we found.

An epigenetic mark hidden inside metamorphosis

2024

Non-CG DNA methylation marks the transition from pupa to adult in Helicoverpa armigera

Royle JW, Hurwood D, Sadowski P, Dudley KJ · Insect Molecular Biology · 6 citations

Why it matters

In insects, DNA methylation is sparse and its purpose is debated — it usually sits in the protein-coding regions of housekeeping genes. Almost nothing was known about how methylation shifts across the dramatic life-stage changes of a metamorphosing insect.

What we did

Working in the cotton bollworm Helicoverpa armigera, a globally significant crop pest, we measured global DNA methylation across larvae, pupae and adults using targeted mass spectrometry, then mapped methylation genome-wide at single-base resolution with whole-genome bisulfite sequencing.

Key findings

Global methylation differed significantly between life stages, and whole-genome bisulfite sequencing pinpointed methylation in the non-CG context as the primary difference between pupa and adult. That non-CG methylation was enriched in genes for key signalling pathways — Hippo, Hedgehog and MAPK — and for ATP-dependent chromatin remodelling.

Significance

The work shows that non-CG methylation — a largely overlooked mark in insects — is dynamically tied to metamorphosis, and flags it as a possible target for integrated pest management of a major agricultural pest.

Kevin's role

Kevin conceived and supervised the study as senior author, and personally led both the whole-genome bisulfite sequencing analysis and the targeted mass-spectrometry quantification of methylation. The work established his Helicoverpa epigenetics research at QUT and was the first project of Jack Royle, the first PhD student he primarily supervised.

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How an ordinary gene became a venom

2023

Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family

Ashwood LM, Elnahriry KA, Stewart ZK, … Dudley KJ, … Prentis PJ · BMC Biology · 12 citations

Why it matters

Sea anemone venoms are a treasure trove of peptides with therapeutic promise — the ShK toxin is a celebrated example — but most anemone toxin families remain uncharacterised, and we rarely catch the moment a gene is recruited into venom.

What we did

We mapped the genomic organisation and evolution of the "sea anemone 8" (SA8) gene family in two species, Actinia tenebrosa and Telmatactis stephensoni, profiled where each gene is expressed, and resolved the structure and function of an SA8 peptide taken from T. stephensoni venom.

Key findings

SA8 genes sit in tight genomic clusters — ten genes across two clusters in one species, six across five clusters in the other. Remarkably, one gene lay inverted within a cluster, and the peptide it encodes had been recruited into venom, expressed in a distinctive tissue pattern resembling toxins used to deter predators. Although mature SA8 peptides share cysteine spacing with ShK, their three-dimensional structure and disulfide connectivity are clearly distinct.

Significance

This is the first demonstration that SA8 is a genuine, distinct gene family in sea anemones, and a vivid case study of how tandem and proximal gene duplication combined with a gene-inversion event can convert a routine gene into a venom component — a rare, concrete window onto venom evolution.

Kevin's role

Kevin generated the sequencing data at CARF that underpinned the genomic and transcriptomic analyses of the SA8 toxin family.

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Rebuilding the genome of plant science's workhorse

2023

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Ranawaka B, An J, Lorenc MT, … Dudley KJ, … Waterhouse PM · Nature Plants · 75 citations

Why it matters

Nicotiana benthamiana is the laboratory workhorse of plant science and molecular farming — used to trial genes, manufacture vaccines and antibodies, and dissect how plants fight off pathogens. Yet its enormous ~3 Gb allotetraploid genome had never been assembled to a high standard, putting a ceiling on the precision of that work.

What we did

We produced high-quality, chromosome-level genome assemblies for the ubiquitously used LAB strain and a related wild accession (QLD), then layered on transcriptome, epigenome, microRNA and transposable-element datasets. Single-nucleotide-polymorphism maps were added for a further two laboratory strains and four wild accessions, giving a true multi-omic reference rather than a bare genome sequence.

Key findings

Despite a turbulent evolutionary history — the loss of five chromosomes from the ancestral tetraploid, expanded intergenic regions, widespread segmental allopolyploidy, advanced diploidization, and recent bursts of Copia retrotransposon activity not seen in other Nicotiana genomes — the two subgenomes still share large blocks of synteny across the Solanaceae. The LAB and QLD lines differ genetically, metabolically and phenotypically (including strikingly different RNA-interference responses) yet remain interfertile and fully amenable to genome editing and both transient and stable transformation.

Significance

The paired LAB/QLD lines give the community a reference partnership with the potential to do for N. benthamiana what the Columbia-0 / Landsberg erecta pair has long done for Arabidopsis — a shared foundation for plant genetics and biotechnology. The paper has already been cited 68 times.

Kevin's role

Kevin generated the long-read genome sequencing data on the PacBio Sequel platform at QUT's Central Analytical Research Facility (CARF), and was primary supervisor of the paper's first author, Buddhini Ranawaka.

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A first genetic blueprint for a prized fishery species

2017

Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus

Rotllant G, Nguyen TV, Sbragaglia V, … Dudley KJ, … Mather PB · BMC Genomics · 16 citations

Why it matters

The Norway lobster is one of Europe's most valuable fishery species and an ecological keystone, yet it had almost no genetic resources — a real gap for sustainable management and for understanding its reproduction.

What we did

We built the first multi-tissue de novo reference transcriptome — no reference genome required — from 16 sequencing libraries spanning both sexes and many tissues: ovary, testis, vas deferens and the masculinizing androgenic gland, plus eyestalk, brain, thoracic ganglia and hepatopancreas. RNA sequencing produced more than 600 million reads, assembled (together with two earlier eyestalk libraries) into 333,225 transcripts averaging 708 bp with an N50 of 1,272 bp. Sex-biased patterns were validated by RT-PCR.

Key findings

Sex-specific transcripts were concentrated in the gonads, followed by hepatopancreas, brain, thoracic ganglia and eyestalk. Among the most highly expressed were a serine/threonine protein kinase in testis and vitellogenin in female hepatopancreas. Most differential expression appeared in gonad and eyestalk tissues, and sex-specific markers were predominantly expressed in males — pointing to sex differences driven by gene regulation in somatic tissues rather than genes carried on sex chromosomes.

Significance

The study delivered the first reference transcriptome for the species — a foundation for reproductive, restocking and fisheries research — and showed that its sex-specific expression is a matter of regulatory control rather than heterogametic sex chromosomes.

Kevin's role

Kevin generated the RNA-seq data and hosted the paper's lead author, Guiomar Rotllant, at CARF over several months — working alongside her to optimise the library preparation and sequencing methods behind the assembly.

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