James Lloyd 🧬

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...

Interesting study suggesting that nucleus, cytoskeleton, and endomembranes preceded acquisition of mitochondria, during eukaryogenesis www.nature.com/articles/s41...

A couple new #PhD opportunities to join my lab at the intersection of #synbio, #plantsci and #biotech as part of the Plant BioDesign doctoral programme spanning the University of York, University of Cambridge, University of Bristol and John Innes Centre. 1/4

Angle dependence as a unifying feature of root graviresponse modules | PNAS Gravitropism, the patterning of postembryonic growth in relation to the gravity vector, allows plants to optimize the use of limited and nonhomogen...

We are really proud to announce the publication of our paper 'Angle dependence as a unifying feature of root graviresponse modules' in collaboration with @universityofleeds.bsky.social @ohiowesleyanuniversity @ista www.pnas.org/doi/10.1073/... @suruchiroy.bsky.social @pnas.org

KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root https://www.biorxiv.org/content/10.1101/2025.11.24.690241v1

Heterochromatin boundaries maintain centromere position, size and number - Nature Structural & Molecular Biology Carty et al. identify the H3K9 methyltransferases that restrict the size and position of the centromere protein A chromatin domain, maintaining functional centromeres.

Very proud to have our latest work now online in
@natsmb.nature.com. A wonderful team effort across the centromere community, across @jansenlab.bsky.social @naltemose.bsky.social @dfachinetti.bsky.social and Giunta labs. Happy reading! 1/4

www.nature.com/articles/s41...

Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast The budding yeast, Saccharomyces cerevisiae, is the workhorse of the brewing industry. Brewers have domesticated a vast array of different strains with traits that complement the beers they wish to br...

Fun new preprint from the lab, headed up by two incredible undergraduate researchers: Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. www.biorxiv.org/content/10.1...

It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖

ARC are considering a restructure in which jobs there will be lost, a source tells me.

This seems ridiculous when they're about to completely overhaul the entire grants system – they've never undertaken anything so large before!

I've long said ARC needs MANY MORE staff, & should do more, not less.

Extreme autotomy and whole-body regeneration in photosynthetic sea slugs Autotomy, the voluntary shedding of a body part, is common among animals. Mitoh and Yusa report an extreme case of autotomy with the shedding of the main body, including the whole heart, and subsequen...

Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?

From: www.cell.com/current-biol...

CloneCoordinate: Open-Source Software for Collaborative DNA Construction Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aide...

Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!

pubs.acs.org/doi/10.1021/...

CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...

And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...

Perspective here:
www.science.org/doi/10.1126/...

I have never seen it in my lab, but when we sent a plasmid to Addgene, they complained a clone had a TE. I don’t know other details. I told them to screen more clones and they found one without it and that was fine.

Probably changing the E. coli host strain might avoid the problem

Super interesting overall and really well explained.

One questions about this post in particular: I thought MTA1 was present in plants and was an RNA MTase. Is this a strange nomenclature thing or something else?

E.g. this paper:

nph.onlinelibrary.wiley.com/doi/abs/10.1...

MTA1‐mediated RNA m6A modification regulates autophagy and is required for infection of the rice blast fungus In eukaryotes, N6-methyladenosine (m6A) is abundant on mRNA, and plays key roles in the regulation of RNA function. However, the roles and regulatory mechanisms of m6A in phytopathogenic fungi are...

Super interesting overall and really well explained.

One questions about this post in particular: I thought MTA1 was present in plants and was an RNA MTase. Is this a strange nomenclature thing or something else?

E.g. this paper:

nph.onlinelibrary.wiley.com/doi/abs/10.1...

Therefore, the Last Eukaryotic Common Ancestor had a dual methylation system: 6mA for transcriptionally permissive chromatin and 5mC for silencing. This dual pattern is maintained in some extant eukaryotes but has diverged in many others, including ALL multicellular groups that lost AMT1. 8/9

But is 6mA directing transcription? We checked in 5 different species across stages and conditions, and we could detect plenty of transcriptional changes not followed by 6mA reprogramming. So correlation does not mean causation (as most times with chromatin features). 5/9

However there's been rampant simplifications across the tree of life. We then took advantage of 6mA basecalling with @nanoporetech.com to profile several eukaryotes branching in very distant groups, some encoding AMT1 or not. AMT1 encoding eukaryotes presented symmetric ApT methylation. 3/9

First we traced the evolutionary history of AMT1 (aka MTA1), the main 6mA enzyme in eukaryotes. We find that a complex repertoire including AMT1 and its heterodimeric partner AMT6/7 can be traced back to the Last Eukaryotic Common Ancestor. Same goes for the RNA methyltransferases METTL3/14. 2/9

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

Two alternative isoforms of PRC2 accessory subunit AEBP2 modulate developmental Polycomb functions in opposite ways - with broadly-expressed AEBP2L acting as an intrinsic inhibitor in somatic cells
@adrianbracken.bsky.social @davidovichlab.bsky.social and colleagues
www.embopress.org/doi/full/10....

I am looking to hire a postdoc interested in combining genetics and evolution to understand why telomeres vary so much in plants. My group has been developing Mimulus a genetic model for studying plant telomeres and we have really cool research brewing. Please check ad for detail. Deadline is 12/31.

Promoter and domain swap analysis delineates heat stress memory-specific determinants of heat shock factor HSFA2 The function of the transcription factor HSFA2 in heat-stress induced transcriptional memory maps to functional domains within the protein.

Latest research from the Bäurle lab on the function of our favourite memory TF - HSFA2!

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes (Fabricio Almeida-Silva, Yves Van de Peer) doi.org/10.1093/plce... #PlantScience @aspbofficial

CREation of an expanded plant memory gene circuit toolkit Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new mol...

I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social

A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.

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

Bioluminescent sentinel plants enable autonomous diagnostics of viral infections Plants engineered with synthetic genetic programs can transform how we monitor and manage the extension of crop pests and diseases. Here, we establish a bioluminescent platform in Nicotiana benthamian...

Such a cool pre-print on making sentinel plants - so much potential!

Bioluminescent sentinel plants enable autonomous diagnostics of viral infections

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

Powerful read processing with matchbox https://www.biorxiv.org/content/10.1101/2025.11.09.685711v1

I’ve only had time to review grants, no papers, this year because I refuse to outsource it to AI and I have been overwhelmed.

Not proud to be slacking my duties. But grants reviewing is a requirement for me, papers are optional. I hope to return to the duty next year.

A proposed model of strigolactone perception in rice.

Strigolactone perception and nutrient responses

#TansleyInsight by Hu et al.

nph.onlinelibrary.wiley.com/doi/10.1111/...

#plantscience

The podcast version of my Raising the Bar talk is now online. If you are interested in "Cosmic Crops" or my work on genetic engineering of plants, please give it a listen (I have not listened to it, I hate listening to myself, so hopefully it is good, but no promises).
soundcloud.com/raising-the-...