Rory Craig

Research Associate: Horizontal Gene Transfer at University of Sheffield Searching for an academic job? Explore this Research Associate: Horizontal Gene Transfer opening on jobs.ac.uk! Click to view more details and browse other academic jobs.

Come work with us!! 2.5 year postdoc on HGT in plants.

Please share and get in touch if interested

www.jobs.ac.uk/job/DPQ418/r...

How do new centromeres evolve while staying compatible with the division machinery?

Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.

👉 doi.org/10.1038/s41586-025-09779-1

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...

Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5

Good question! Auxenochlorella have been sampled from seawater (especially A. symbiontica), but to my knowledge they are only known as symbionts of freshwater hydra and sponges. But they could be useful to investigate the molecular basis of these symbioses

This Halloween, we have a spooky evolutionary story for you.
The brainchild of @delaconcepcionjc.bsky.social, Nick Irwin and our fantastic collaborators is now out in @natplants.nature.com www.nature.com/articles/s41...
Here’s why I love this work — and why I think you’ll enjoy it too. 👇

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

www.biorxiv.org/content/10.1...

(6/6) Overall, we found that the “yeast-like” processes of allodiploid hybridisation, mitotic recombination, loss-of-heterozygosity and aneuploidy all occur in an alga, showing the generality of these forces to vegetatively diploid eukaryotes

(5/6) We also saw aneuploidies in two strains and we successfully transformed a trisomic chromosome using an allele-specific construct. We’re hopeful that we can utilise these redundant chromosomes for synthetic biology by sequential introduction of transgenes

(4/6) Most remarkably, our reference strain UTEX 250 is an allodiploid hybrid of two close relatives, A. protothecoides and A. symbiontica, that are distinguished by highly rearranged karyotypes. The UTEX 250 sub-genomes have been further shuffled by rearrangements and recombination

(3/6) Unlike most green algae, Auxenochlorella are vegetatively diploid and their genomes are shaped by evolutionary phenomena that reflect this. While these processes are well-understood in yeast, we were surprised to see extensive mitotic recombination and loss-of-heterozygosity in several strains

(2/6) We introduce selectable markers, inducible promoters and fluorescent reporters for protein localisation, and @marcoaduenas.bsky.social has written a protocol for HR-based transformation: dx.doi.org/10.17504/protocols.io.x54v922mql3e/v1. All credit to a team led by Jeff Moseley here

(1/6) First and foremost, Auxenochlorella spp. are oily green algae that can be readily transformed by homologous recombination, enabling efficient site-specific transformation of the nuclear genome. This is a first for chlorophytes, and we hope that it will facilitate lots of interesting research

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella Auxenochlorella, green algae shaped by evolutionary forces acting on vegetative diploids, are amenable to discovery research and bioengineering via efficie

Excited to introduce Auxenochlorella as a new algal reference organism for fundamental plant science and bioengineering. A paper in two parts: a genetic toolkit for site-specific genomic manipulation, paired with the most unusual genome I’ve ever worked on

academic.oup.com/plcell/artic...

Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes https://www.biorxiv.org/content/10.1101/2025.10.23.681605v1

So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:

rdcu.be/eITQH

Fortunate to have played a small role in this project led by @caroleduchene.bsky.social. Phaeoviruses likely integrate into their host genomes using a promiscuous tyrosine recombinase, before reactivating in reproductive cells. Exciting to see diverse latency mechanisms emerging for giant viruses