For actually constructing phylogenetic trees, I have compiled this separate repository which I have written over several years with advice and best practices for constructing phylogenetic trees. Any feedback on this is also welcome! github.com/davidjhoey/p...

GitHub - davidjhoey/plantphylo: Molecular phylogenetics guide for the assembly of gene trees. A guide to identifying homologous genes and constructing trees with command line tools. Intended as a prac...

Molecular phylogenetics guide for the assembly of gene trees. A guide to identifying homologous genes and constructing trees with command line tools. Intended as a practical guide and a teaching re...

github.com

Introducing PhyloDig: a small command-line tool I am developing to make comparative phylogenetic analyses easier. github.com/davidjhoey/P...

GitHub - davidjhoey/PhyloDig: PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam d...

PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam domain filtering, and sequen...

github.com

Evaluating cacao pod resistance to black pod disease caused by three Phytophthora species https://www.biorxiv.org/content/10.64898/2026.09.17.752234v1

Palette—a system for visualizing the expression levels of target genes in orchids (Zhenyu Yang , Su Ni , Qiyu Zhang , et al) doi.org/10.1093/plph... #PlantScience @aspbofficial

Palette—a system for visualizing the expression levels of target genes in orchids

By blending two types of plant pigments like an artist mixing colors on a palette to create new flower colors using multiple genetic transformation methods

doi.org

Plant-Microbe enthusiasts! The next Road to Jeju Legends of ISMPMI series speaker is Jonathan Jones. The webinar is free to attend, but you must register: uchicago.zoom.us/webinar/regi... Attend live on September 30, 2026 3pm UTC or watch it later on the ismpmi.org.

There's still time to join us for the 2026 Sainsbury Laboratory Symposium on 22-24 September (#SLS26)! This year's Symposium theme is Shaping Life: Mechanisms of Morphogenesis and is coordinated by Sarah Robinson and Neha Bhatia. www.slcu.cam.ac.uk/sainsbury-la...

The aphid effector CathB6 suppresses EDS1-dependentimmunity and rewires MORF2-GUN1-GLK signalling tosustain host cellular homeostasis in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.08.10.743731v1

Concurrent session submissions for the 2027 IS-MPMI Congress in Jeju (July 18-22) are now open! Contribute to the dynamic scientific program and engage the international plant–microbe interactions community in Jeju, South Korea. Apply by 25 Sept. ismpmi.org/announcement...

Super useful! Keep your Marchantia clean everybody!

Darius Kosmützky@dariuskos.bsky.social · 2mo ago

Ever had issues with contamination in #Marchantia or #liverwort tissue culture? We've developed a protocol that is simple and low-effort (albeit slow) to get rid of fungi and bacteria: dx.doi.org/10.17504/pro.... Work led by Isaac Coven and supported by Chetan Pandey, myself & @dromius.bsky.social.

Ever had issues with contamination in #Marchantia or #liverwort tissue culture? We've developed a protocol that is simple and low-effort (albeit slow) to get rid of fungi and bacteria: dx.doi.org/10.17504/pro.... Work led by Isaac Coven and supported by Chetan Pandey, myself & @dromius.bsky.social.

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

A tomato MIK2‐clade receptor is involved in the perception of a Fusarium‐derived elicitor - Maroschek - New Phytologist - Wiley Online Library nph.onlinelibrary.wiley.com/doi/10.1111/...

A tomato <fc>MIK2</fc>‐clade receptor is involved in the perception of a <fi>Fusarium</fi>‐derived elicitor

Fusarium elicitor responsivness and MIK2-clade proteins are conserved across plant families.

nph.onlinelibrary.wiley.com

Preprint! How do "friendly" rhizobia build a legume nodule? @albinteulet.bsky.social found that some may carry hidden transcription factors - proteins that mimic DNA-binding folds to enter the plant nucleus and rewrite its developmental program. www.biorxiv.org/content/10.6... (1/6)

There is some research into growing edible liverworts (Marchantia polymorpha). phys.org/news/2026-01... That would work in a Mars greenhouse context.

Q&A: Is liverwort humanity's savior? Possibilities in food and medicine

Research on using Marchantia polymorpha, commonly known as liverwort, a plant closely related to moss, for food and as an ingredient in medicine and supplements is being conducted at Kobe University.

phys.org

Growing love - when a root meets a symbiotic #Mycorrhiza #fungus See what happens with MycorRhize3D. schornacklabslcu.github.io/MycorRhize3D/ Simulate a tap root in soil with spores. Roots turn red when colonised, just like in this paper journals.plos.org/plosbiology/... Reply for suggestions!

The 'heart' of the #Mycorrhiza #fungi #symbiosis is the arbuscule where plant and fungus exchange nutrients and carbon. Try the arbuscule growth simulator. Let me know how you adjust parameters to get the most beautiful arbuscules. schornacklabslcu.github.io/Arbuscule-Sim/

Happy to share some of the auxin Marchantia research we've been working on for a while with @fromani.bsky.social and @jimhaseloff.bsky.social. We confirm long standing suspicions that stem cells in Marchantia exist in an auxin concentration/signalling minimum, and potentially a cytokinin maximum.

Marchantia stem cell maintenance and re-establishment are controlled by MpPIN1-mediated auxin transport and ARF signalling

Meristem organization in land plants depends on coordinated auxin distribution, transport and response, yet how these processes are integrated during vegetative growth of the gametophyte of non-seed p...

biorxiv.org

Anthropic’s AI for Science Program Apply by 15 July www.anthropic.com/news/claude-... Application form: docs.google.com/forms/d/e/1F...

Claude Science, an AI workbench for scientists

Claude Science is a customizable app that integrates the tools and packages researchers most often use, produces auditable artifacts, and provides flexible access to computing resources.

anthropic.com

Important news! The new ISMPMI website is live! Visit the site to get society news, watch posted videos, listen to our podcasts, become or manage your membership and more. ismpmi.org

IS-MPMI - International Society for Molecular Plant-Microbe Interactions

Diverse Backgrounds Common Interests Connecting leading scientists and researchers around the world in microbiology, nematology, plant pathology, developmental biology, genetics, genomics, proteomics,...

ismpmi.org

Registration is now open for our next Road to Jeju Webinar featuring Rising Stars of IS-MPMI. lnkd.in/gMeN7F94 Join us on July 29. Speakers will be announced soon. Thanks to our sponsors GetGenome, Shanghai Tanon Life Sciences, and the British Society for Plant Pathology.

‼️Job altert🚨📢 please spread the word: We're looking for a postdoctoral researcher to join our new department "Phytopathology and Plant Protection" at @unihalle.bsky.social. www.verwaltung.uni-halle.de/DEZERN3/AUSS...

Attention ECRs: Deadline for self nominations to present in the next Rising Stars of IS-MPMI @ismpmi.bsky.social webinar is TODAY! PhD students and postdocs — don't miss your chance to share your research with the global MPMI community! Apply now: docs.google.com/forms/d/e/1F...

Self nomination form for Rising Stars of IS-MPMI Early Career Webinar Series July 29th 2026

Sponsored by GetGenome

docs.google.com

How plants form their stomata – and are thereby able to save water, was described in May by a team of plant scientists around Christopher Grefen and Khushbu Kumari , from @ruhr-uni-bochum.de DOI: 10.1093/plcell/koag150 news.rub.de/english/pres...

New Paths for Developing Drought-resistant Crops

Researchers are discovering how plants form their stomata – and are thereby able to save water. This insight could open up new paths for more drought-resistant plants.

news.rub.de

Very happy this is now published in full! Symbiotic phosphate transporter dynamics in rice expose functional plasticity of the arbuscules www.nature.com/articles/s41... A thread of some of our findings (and timelapses) below 🧵🔬🎥

Defining the Xanthomonas euvesicatoria type II-secreted effector arsenal: core nutritional functions and effector diversity @ericksonlab.bsky.social @biorxivpreprint.bsky.social doi.org/10.64898/202...

This Wednesday: Roger Innes opens the Road to Jeju webinar series! "Leaf surface RNA: How does it get there and what does it do?" Decades of foundational work on plant immunity. Road to Jeju is supported by @getgenome.bsky.social, with this seminar sponsored by @newphyt.bsky.social 🌱 Register 👇

Conserved symbiosis-associated genes in the cycad Encephalartos natalensis suggest co-option for cyanobacterial symbiosis nph.onlinelibrary.wiley.com/doi/10.1111/...

Marchantia has two RBOHs. Double mutant = disorganized cell mass. Conditional mutant analyses show they are required to sustain morphogenesis via cuticle-cell-wall integrity. Clever study. www.sciencedirect.com/science/arti...

Indispensable roles of RBOH-mediated ROS production in development and morphogenesis of Marchantia polymorpha

Reactive oxygen species (ROS) are now well established as essential signaling molecules in eukaryotes. In plants, NADPH oxidases, known as respiratory…

sciencedirect.com

Happy to share our newest preprint. We developed guidelines and analysis workflows for FLIM Imaging in plants. Multiplexing with spectrally overlapping fluorophores in plants is now possible. Have a look. Any feedback is more than welcome. www.biorxiv.org/content/10.6...

Homology of the dark cells of Paleozoic liverworts with the specialized oil body cells of modern liverworts (Marchantiophyta) Tremblay and Mercadal nph.onlinelibrary.wiley.com/share/BWYYSE...