Naples Botanical Garden. Visit Two. Part Two.

Updated preprint: "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae" doi.org/10.1101/2025... #Evolution #Pigments #Genomics #Bioinformatics @nancy-choudhary.bsky.social @bpucker.bsky.social @unibonn.bsky.social

Phylogenomic approach uncovers the hybrid origin and biogeographic diversification of the plum genus doi.org/10.1101/2023... Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae doi.org/10.1101/2025...

A New Cost Effective, Simplified Workflow for Transposon Insertion Sequencing (TIS) doi.org/10.64898/202... Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis doi.org/10.1101/2021... #Genomics #Bioinformatics

Mountains rise above South Saint Vrain Creek in Indian Peaks #FallBack to July 23 🌿 BlueSky FOREVER!

Left: Kalanchoe marnieriana, normally does not produce plantlets, but when leaves are detached, they sprouts plantlets but no roots from wound site. Right: Kalanchoe crenata doesn’t produce plantlets at all. Instead detached leaves readily regenerate roots from wound site. #PlantScience

New paper + new mug = official celebration 🎉☕ Here is Jakob with our review: “Diversity and ecological functions of anthocyanins” doi.org/10.1186/s128... Paper mugs are a tradition in our group — and this one is well earned. Congrats! 🌸🔬 #Anthocyanins #Pigments #Flavonoids #Evolution

FastSpeciesTree: Fast and Scalable Species tree Inference doi.org/10.64898/202... Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae doi.org/10.1101/2025...

T2T and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres doi.org/10.64898/202... Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana doi.org/10.1101/2024...

Pangenome Analysis of Pyrus Reveals Potential Role of Transcription Factors in Recent Adaptation to Arid Environments doi.org/10.64898/202... Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet doi.org/10.1101/2023...

Two weeks in, and the Python course participants are officially starting their own projects 🐍✨ From fundamentals to hands-on bioinformatics—now the fun really begins. Slides: github.com/bpucker/teac... #Python #Bioinformatics #Education @puckerlab.bsky.social

On the correctness of gene tree tagging and the consistency of ASTRAL-pro under a unified model of gene duplication, loss, and coalescence doi.org/10.64898/202... DupyliCate - mining, classifying, and characterizing gene duplications doi.org/10.1101/2025...

Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation doi.org/10.1101/2024... Cookbook for Plant Genome Sequences www.doi.org/10.20944/pre... #Genomics #Bioinformatics #PlantSciences

Argynnis cybele carpenterii, a subspecies of the Great Spangled Fritillary, on Cutleat Coneflowers, East Fork San Juan #nativeplants #FallBackFlowers #FallBack to July 19 🌿

We published our open-access review on anthocyanins in BMC Plant Biology! 🌿🔬 From antioxidants to ecological roles in nature, these pigments are way more than pretty colors. Check it out👇 🔗 doi.org/10.1186/s128... 📸 Here is Nele celebrating this achievement! #PlantScience #Anthocyanins #OpenAccess

The PacBio PAG 2026 party has begun! 🎉🌱🐄 We’re excited for a night of great conversation, connections, and celebrating the collaborations that make plant and animal genomics so inspiring. #PAG33 #PacBio #PAG2026

Two great conferences our group attended this past week: #PAG33 an international plant agriculture genomics conference and #TICA Digital Frontiers, a sunflower family-focused exploration of international collaborations and cutting-edge science. Plus a fantastic tour of the herbarium and labs at BRIT

The other, also from the wise and awesome Brandon Gaut, was to start writing your paper now. No, yesterday. Starting writing sooner than you think you should helps you see the story, which saves you a ton of time in the long run.

Looking for genome sequences, annotations, or expression data from @puckerlabpapers.bsky.social ? Access large datasets on bonndata: 🔗 www.izmb.uni-bonn.de/en/pbb/resea... #OpenScience #Genomics #ResearchData #Bioinformatics #GenomeData @bpucker.bsky.social @opensciene-unibonn.bsky.social

A drought stress-induced MYB transcription factor regulates pavement cell shape in leaves of European aspen (Populus tremula) doi.org/10.64898/202... Automatic identification and annotation of MYB gene family members in plants doi.org/10.1101/2021... #PlantSci #TranscriptionalRegulation

ProteoCast: a web server to predict, validate, and interpret missense variant effects doi.org/10.1101/2025... NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718 #Protein #Diversity #Variation

Conservation of non-consensus nucleotides in transcription factor binding sites doi.org/10.64898/202... Automatic identification and annotation of MYB gene family members in plants doi.org/10.1101/2021... #TranscriptionFactors #GeneExpression

Sweet signals: Using floral traits to predict nectar sugar availability doi.org/10.64898/202... Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation doi.org/10.1101/2024... #Genomics #Evolution #Ecology

Arabidopsis TITAN LIKE is required for U12-type intron splicing, especially for AT–AC subtypes doi.org/10.1101/2025... Animal, fungi, and plant genome sequences harbour different non-canonical splice sites doi.org/10.1101/616565 #Genomics #Bioinformatics

We have an open POSTDOC position to explore Marchantia immune receptor biology that is closing on the 18th of Jan. Apply using the link below, and/or email me for more details. www.jic.ac.uk/vacancies/po...

Pitcher Plants Fine-Tune Their Deadly Pools for Maximum Carnivory botany.one/2026/01/pitc... Carnivorous pitcher plants actively regulate their digestive fluid levels to maintain the perfect trap, not too full and not too empty, scientists discover.

Mitella stauropetala, our Side-Flowered Mitrewort, blooming on the Rocky Fork Trail #nativeplants #FallBackFlowers #FallBack to July 13 🌿

We mostly talk about real trees here and at Our Trees. Here is a brief discussion of the Tree of Life and its first use in 1837 by Charles Darwin to describe evolutionary relationships. Have a look.

Why is there a tube on every monitor in our Python course? 🐍 It is a simple progress signal: students put the tube up while working on exercises and take it down when they are finished. This makes it easy to see who is still working and who is ready for the next step. @puckerlab.bsky.social

Join the PacBio Scavenger Hunt at #PAG33! 🌱🐱 Pick your side – Team Plant or Team Animal – track down clues, earn points, and explore how PacBio tech is illuminating biology across species. Register: bit.ly/4qqbywk#PAG33 Questions? Stop by Booth #219!

🌱 Plant Speak: Species 🌱 In biology, a species is the principal subdivision of a genus, regarded as the fundamental unit of classification. Members of a species resemble one another and can breed among themselves, but not with members of other species. 🌸 #PlantSpeak #KnowYourPlants #BotanyBasics

Phacelia formosula, our endemic endangered Northpark Phacelia, blooming above the Laramie River south of Jelm #nativeplants #FallBackFlowers #FallBack to July 12 🌿

“Analysis of Biological Data with Python” started today for biology bachelor students 🧬🐍 Want to learn Python for data analysis? Slides are freely available: github.com/bpucker/teac... #Python #DataAnalysis #Biology #OpenScience #BigData #Bioinformatics #DataScience @puckerlab.bsky.social

We’re in San Diego for #PAG33! 🐾 🌱   Stop by #PacBio Booth 219 to see live Vega demos and explore how HiFi sequencing is driving breakthroughs in plant, animal, and microbial genomics. Connect with our experts and see what’s possible! Details: bit.ly/48O6aLU

Check out this growth difference in just 20 days! I've been feeding these flytraps with synthetic time release fertilizer in their traps (nutricote). I can't avoid seeing them as Arnold in his peak steroid days...

I #amwriting today about the extent of orchid coverage across Britain & Ireland - the range of habitats in which they flourish, and the extent of the boundaries they push, from the north of Shetland to the English south coast, from East Anglian shores to the west of Ireland. @bsbibotany.bsky.social

My friend Kate Armstrong, @brainchain.ca, asked us to post pictures of roses, #PostMoreRoses, but in my catalog of over 200,000 botanical photos, there is not a single one of a rose. If we broaden to the family Rosaceae, we have this nice pear flower in the rain.

Friendly face in the garden just now. #hellebore #GardenLife

Considering the disgusting things going on over at X: Why doesn’t the EU apply the precautionary principle??? It never hesitated to ban other inventions that pose zero danger to the community with this principle.

@annapardo-phd.bsky.social is a computational biologist who studies plant genomics and abiotic stress responses. Her recent work in #G3journal identified genes related to common stress physiology responses as well as stress-related transcription factors. 9/19🧵

Alex Zaccaron is unlocking how organisms evolve to overcome host resistance. Join his talk at #PAG to learn how he is doing this by comparative genomics and transcriptomics using Oxford Nanopore sequencing of fungal plant pathogens. https://bit.ly/3Xt9RS7

Are you working on ancient plant DNA? 🌿 We are organising a symposium on Ancient plant genomics at #SMBE2026 in beautiful Copenhagen 🇩🇰 Join Nathan Wales, Shuya Zhang, Marcela Sandoval Velasco, me, and our fantastic speaker Logan Kistler from the Smithsonian Institution. Help us spread the word!

100% this!👇

FLOWERS/BLUIMARY.GIF

AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data doi.org/10.1101/2025... NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718

What is the major role of anthocyanins—painting flowers, acting as sunscreens, responding to stress, or defending against pathogens? Our latest paper dives into the diversity and ecological functions of anthocyanins 🌈🌿 doi.org/10.1186/s128... #PlantSciences #Anthocyanins @bpucker.bsky.social

Cladonia #lichen. #Newfoundland, Canada. #fungi #fungifriends

Some houseplants for today. #BlueSkyArtShow #Vibrant

Read the article here: https://learndirt.com/learn/hugelkultur-mistakes/