The project combined publicly available RNA sequencing data with the reference genome of Cycas panzhihuaensis. Paired-end Illumina reads were assembled into transcriptomes, from which protein-coding regions were predicted and orthologous gene families were identified. The researchers applied a relaxed single-copy strategy, retaining loci present in at least 75% of the 346 cycad accessions and allowing no more than 10% to carry a second copy. This produced 1,409 nuclear loci with average taxon occupancy of 94.9%, compared with only 115 loci under a strictly single-copy approach.

Each locus was aligned independently, and regions that were poorly aligned or rich in gaps were removed. IQ-TREE then inferred a gene tree for every locus, with phylogenetic pruning used where accessions contained multiple copies. A partitioned maximum-likelihood analysis treated all 1,409 loci as independent partitions, each with its own best-fit substitution model. The concatenated alignment contained 411,345 amino-acid sites. Support was assessed with 1,000 ultrafast bootstrap replicates, while gene and site concordance factors measured how individual gene trees and alignment sites supported each branch.

The resulting backbone placed Dioon as sister to the remaining Zamiaceae. The other zamiads formed two principal clades: Encephalartos, Lepidozamia and Macrozamia in one, and Bowenia, Stangeria, Ceratozamia, Microcycas and Zamia in the other. Every genus had 100% ultrafast bootstrap support and crown-node gene concordance factors of 62% to 81%. The Microcycas–Zamia relationship had the strongest genomic support among the intergeneric nodes, with a gene concordance factor of 66.7% and a site concordance factor of 85.5%.

Support was less uniform for other relationships. Although 240 of 344 scored internal branches, or 69.8%, had bootstrap support of at least 95%, and the median bootstrap value was 100%, the median gene concordance factor was only 3.2%. A total of 272 nodes, or 79.1% of the scored internal branches, had gene concordance below 10%. Site concordance was generally higher, averaging 40.3%, and approximately 71% of scored nodes exceeded the 33.3% expectation under random quartet resolution. The placements of Bowenia and Stangeria were comparatively weak, with gene concordance factors of 11.6% and 16.1% and site concordance factors of 33.8% and 36.8%.

The study links the contrast between high bootstrap values and low gene concordance to the kind of signal contained in the individual loci. The dominant pattern of discordance was polyphyly, with a mean gene-tree failure proportion of 89.0%, rather than strong support for an alternative resolution, whose mean values were 1.6% for the first alternative and 1.7% for the second. The authors note that slow molecular evolution characteristic of gymnosperms, together with recent diversification within cycad genera, can leave short internal branches with too few substitutions for individual loci to resolve confidently. Concatenation across 1,409 loci can still provide strong support for the overall topology.

Divergence times were estimated by penalized likelihood in TreePL after Ginkgo was pruned from the tree, with 12 minimum–maximum age constraints. Five constraints were derived from a fossil-calibrated total-evidence analysis, while seven were secondary genus-level calibrations taken from confidence intervals in recent molecular dating studies. Gene-wise bootstrap resampling was performed 100 times, with the 1,409 loci resampled with replacement and branch lengths re-optimized on the fixed maximum-likelihood topology, to calculate 95% confidence intervals for all 345 internal nodes. The mean width of these intervals was 3.97 million years.

The time-calibrated tree placed the Cycadales crown at approximately 359 million years, with a 95% confidence interval of 320–359 million years. This estimate reached the upper calibration bound and was consistent with the Carboniferous–Permian age inferred from the fossil record. The Zamiaceae crown was estimated at approximately 194 million years, with a 95% confidence interval of 165–196 million years. Backbone divergence estimates generally occupied 28% to 66% of their permitted calibration intervals, indicating that molecular branch lengths contributed to those ages rather than the bounds alone determining them.

Estimates for the crowns of individual genera were less independent of their constraints. Six of the seven genera with crown calibrations converged on the maximum permitted age: Dioon at 57 million years, Cycas at 40 million years, Lepidozamia at 34 million years, Zamia at 33 million years, Macrozamia at 29 million years and Encephalartos at 27 million years. Ceratozamia was the exception. Its estimated crown age of 32 million years, with a 95% confidence interval of 25–33 million years, fell within its 13–36 million-year calibration range and was interpreted as more directly informed by the molecular data. The authors caution that rate smoothing can push ages toward older values across short branches associated with recent radiations.

All trees and supporting data have been archived in Zenodo and linked to the World List of Cycads, where the phylogram and timetree can be explored through an interactive display. The public resources include the maximum-likelihood tree with branch lengths, bootstrap and concordance values; the dated tree with confidence intervals; 1,409 individual gene trees; and the concatenated alignment, partition definitions, support values and calibration data. Tip labels use accepted taxonomic names, allowing tree tips to be connected directly to the World List’s species records. The framework can support taxonomic evaluation, identification of species groups needing denser population sampling, trait mapping, biogeographic analysis and conservation calculations based on phylogenetic diversity or evolutionary distinctiveness.

Subject of Research: Species-level phylogenomic relationships and divergence times of the 10 extant cycad genera

Article Title: A comprehensive phylogenomic framework for cycads ( Cycadales )

Article References: Calonje, M., Clugston, J. A. R., & Coiro, M. (2026). A comprehensive phylogenomic framework for cycads (Cycadales). PhytoKeys, 275, 81-95. https://doi.org/10.3897/phytokeys.275.194283

Image Credits: AI Generated

DOI: 10.3897/phytokeys.275.194283

Keywords: cycads, Cycadales, phylogenomics, phylotranscriptomics, molecular dating, gene concordance, Zamiaceae, Cycadaceae, plant evolution, open genomic data, comprehensive, phylogenomic

Amanita is the largest genus in the family Amanitaceae, encompassing roughly 650 species and divided taxonomically into three subgenera and eleven sections. Different sections produce strikingly different toxins. The notorious death cap, Amanita phalloides, and its relatives in section Phalloideae cause fatal liver damage through amatoxins such as alpha-amanitin. Species in sections Amidella and Roanokenses, including A. proxima and A. smithiana, inflict kidney injury through aminohexadienoic acid. Section Amanita, by contrast, is the home of the neurotoxic isoxazoles: ibotenic acid, which mimics the neurotransmitter glutamic acid and stimulates NMDA receptors, and muscimol, its decarboxylation product, which mimics gamma-aminobutyric acid and activates GABA receptors. Together these compounds produce the central nervous system excitation, confusion, and hallucinations characteristic of fly agaric poisoning, and they have been implicated in severe intoxications and even fatalities across Asia, Europe, and North America.

Historically, the psychoactive reputation of A. muscaria was attributed to muscarine, the alkaloid first isolated from the species in 1869, which binds acetylcholine receptors and mimics parasympathetic nervous system stimulation. But muscarine is present in fly agaric at only around 0.0003 percent by weight, far too little to cause intoxication, while in some mushrooms of the families Clitocybaceae and Inocybaceae concentrations can reach 1.6 percent. Ibotenic acid and muscimol, isolated in the 1960s, were eventually recognized as the true active agents. Until recently, however, the biosynthetic machinery behind these isoxazoles remained obscure. That changed when Obermaier and Müller elucidated two alternative pathways in A. muscaria that convert glutamine or glutamate into ibotenic acid and muscimol using seven core enzymes, encoded by the genes iboA, iboC, iboD, iboF, iboG1, iboG2, and iboH, arranged contiguously in a biosynthetic gene cluster.

Biosynthetic gene clusters of this kind, which in fungi also underlie the production of compounds as consequential as penicillin, lovastatin, cyclosporin, psilocybin, and the aflatoxins, are ideal evolutionary markers because their presence or absence can be traced directly in genome data. The research team, led by Chinese mycologists working with specimens archived in herbaria at Hunan Normal University and the Kunming Institute of Botany, collected 101 Amanita fruiting bodies between 2006 and 2022 across Central, Eastern, Northeastern, Southern, and Southwestern China. Ninety-nine of these represented 29 species of section Amanita, including 26 described species and three newly encountered unnamed species, providing sampling that spans essentially every major lineage of the section known worldwide.

Reconstructing the evolutionary framework demanded multiple tiers of analysis. The team first built barcode trees from the standard fungal DNA markers ITS and LSU, covering 75 species of section Amanita globally, and then a five-locus tree adding the nuclear genes RPB2, TEF1, and TUB2 for the 29 Chinese species. These analyses resolved three major clades within the section, but several internal relationships remained statistically shaky. To break through this ambiguity, the researchers sequenced 25 whole genomes on an Illumina NovaSeq platform, assembled them de novo, identified 467 shared single-copy genes, and concatenated nearly 293,000 aligned amino acid positions into a phylogenomic matrix. The resulting species tree achieved 100 percent bootstrap support at essentially every node, definitively resolving the previously tangled subclades of the species-rich Clade A and cementing the framework onto which toxin data could be mapped.

With the tree in hand, the team searched the 25 genomes for homologs of the seven ibo genes using the known sequences from A. muscaria as queries, retrieving 134 genes in total. The results were strikingly clean: ibo genes were present in 21 species, all belonging to a single strongly supported monophyletic clade, Clade A, and entirely absent from species in the other two clades of the section. In 17 species all seven genes were recovered, while in four species a subset was missing, most plausibly because DNA degradation in dried museum specimens fragmented the genome assemblies rather than because the genes are truly gone; one such species, A. griseopantherina, is known to produce muscimol, which would be impossible without a complete cluster. Amino acid identities of the ibo proteins ranged from about 70 to 97 percent relative to fly agaric, with most exceeding 80 percent, consistent with a shared ancestral origin.

Muscarine told a complementary story. Using ultrahigh-performance liquid chromatography coupled to tandem mass spectrometry, the team screened all 101 dried samples, detecting muscarine in 22 samples representing eight species: A. concentrica, A. flavopantherina, A. ibotengutake, A. muscaria, A. orientigemmata, A. pseudosychnopyramis, A. parvisychnopyramis, and A. subfrostiana. These eight form a small, fully supported monophyletic subclade nested within Clade A, and muscarine was found nowhere else in the section. Beyond the two species previously known to contain the alkaloid, six species are documented here for the first time. The concentrations, expressed on a dry-weight basis, ranged from just over 1 to a remarkable 6,428.57 milligrams per kilogram in A. concentrica, a level comparable to the most muscarine-laden members of the Clitocybaceae and far above what has ever been reported in fly agaric itself.

Molecular dating using a Bayesian relaxed-clock approach added the temporal dimension. Calibrating against the Cretaceous split between Amanitaceae and Pluteaceae, estimated at around 113 million years ago, the analysis placed the origin of the genus Amanita at roughly 96 million years ago and of section Amanita at about 45 million years ago. The ibotenic acid gene cluster was acquired approximately 28 million years ago, with muscarine biosynthesis emerging later, around 15 million years ago, in the ancestor of the small subclade. Crucially, the monophyletic distributions with no detectable losses indicate that each toxin system evolved once and was faithfully retained as its bearer species diversified. Gene-by-gene trees showed partial topological conflicts with the species tree, suggesting recombination, duplication, or loss events within the cluster, a pattern that echoes conflicts reported for the amanitin biosynthetic genes in section Phalloideae and contrasts with the tidy congruence observed for the psilocybin cluster in Psilocybe.

The practical implications are sobering. Because muscarine’s estimated lethal dose for humans falls somewhere between 40 and 495 milligrams depending on the source consulted, a kilogram of fresh A. concentrica could in principle deliver a fatal dose of muscarine alone, without any contribution from ibotenic acid or muscimol. In Chinese fly agaric samples, muscarine reached 84 to 474 milligrams per kilogram, orders of magnitude above earlier assumptions that had led clinicians to dismiss the alkaloid in this species. Patients poisoned by members of the doubly armed subclade may therefore present overlapping central and parasympathetic symptoms, and the study’s integrated genetic and chemical map now gives healthcare providers a rational basis for anticipating which toxin profiles to expect from which mushrooms. It also parallels the pattern seen in Clitocybaceae, where muscarine likewise arose once around 20 million years ago and persisted, while in Inocybaceae the trait has evolved and been lost repeatedly. As genome-scale phylogenetics continues to replace single-locus barcoding, the hidden evolutionary architecture of fungal toxins, once murky, is coming sharply into focus, and with it a far better understanding of one of nature’s most consequential chemical arsenals.

Subject of Research: Evolutionary origins and distribution of neurotoxin biosynthetic gene clusters in Amanita section Amanita

Article Title: The distribution and evolution of muscarine and the ibotenic acid biosynthetic gene cluster within the genus Amanita section Amanita revealed by phylogenomics

Article References: Su, Y.-T., He, Z.-M., Yang, Y.-Z., Xu, F., Lai, M.-M., Yang, Z. L., Zhang, P., & Chen, Z.-H. (2026). The distribution and evolution of muscarine and the ibotenic acid biosynthetic gene cluster within the genus Amanita section Amanita revealed by phylogenomics. IMA Fungus, 17, Article e175874. https://doi.org/10.3897/imafungus.17.175874

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.175874

Keywords: Amanita, mushroom toxins, ibotenic acid, muscimol, muscarine, biosynthetic gene cluster, phylogenomics, mycology, molecular dating, fly agaric, mushroom poisoning, secondary metabolites

Sphingolipids are a class of lipids built around a sphingoid base rather than the glycerol backbone found in ordinary fats. At their center sit ceramides, molecules composed of a long-chain base linked to a fatty acid through an amide bond. In eukaryotic cells, ceramides and their derivatives are far more than structural padding for the plasma membrane. They participate in growth, survival, differentiation, stress adaptation, and signaling, and their synthesis and breakdown form one of the most intricate metabolic networks in the cell. In fungi, the predominant sphingoid base is phytosphingosine, and the complex sphingolipids built on it, such as glycosyl inositol phosphoceramide, are essential constituents of the outer leaflet of the plasma membrane, where they modulate signal transduction, cell adhesion, and cell cycle progression.

Despite this importance, nearly everything scientists know about fungal sphingolipid metabolism comes from a narrow slice of fungal diversity, the Dikarya, which includes the familiar yeasts, molds, and mushrooms. For the vast majority of fungal lineages, the enzymes involved in ceramide biosynthesis and recycling had never been systematically cataloged. To close that gap, the research team assembled protein sets from 148 early diverging fungi and representatives of 35 classes of Dikarya, downloaded from NCBI in May 2022, and screened them against reference sequences drawn from the UniProt and REACTOME databases. Using domain-based clustering with the CLANS algorithm, followed by domain architecture prediction with Pfam and InterProScan, the researchers identified 34 protein families that they subdivided into 59 subfamilies spanning the full sphingolipid pathway.

The 59 subfamilies fall into three main pathway groups: seven involved in de novo ceramide synthesis, 22 in ceramide recycling, and 30 in cooperating pathways that include fatty acid metabolism, sterol metabolism, glycoprotein modification, and lipid transport. The analysis revealed a fundamental split in how these groups have evolved. Five of the seven de novo synthesis subfamilies and 19 of the 30 cooperating pathway components are conserved across all fungi, reflecting their ancient, housekeeping roles. In contrast, roughly half of the ceramide recycling proteins vary between phyla, suggesting that this arm of the pathway has been a playground for evolutionary experimentation.

None of the fungal phyla possesses all 59 subfamilies, and the diversity varies dramatically across the tree. Glomeromycota and Mucoromycota lead with 44 subfamilies each, followed by Chytridiomycota with 42, Blastocladiomycota with 41, and Mortierellomycota with 40. At the other extreme, Microsporidia, obligate intracellular parasites, retain just 9 subfamilies, preserving only the core de novo ceramide and fatty acid synthesis pathways while losing complex sphingolipid metabolism entirely. This reduction likely represents an adaptation to anaerobic parasitism, in which the parasites rely on host-derived fatty acids and shed the metabolic machinery they no longer need. Similarly reduced repertoires appear in the anaerobic gut fungi of the Neocallimastigomycota and in the parasitic Rozellomycota.

One of the most striking findings concerns the difference between flagellated fungi, which include the Chytridiomycota, Neocallimastigomycota, and Blastocladiomycota, and their non-flagellated relatives. Flagellated fungi show a consistent reduction in the diversity of sphingolipid recycling enzymes, including acid sphingomyelin phosphodiesterase, acid ceramidase, lysosomal acid glucosylceramidase, sphingolipid C9-methyltransferase, and several glycosyltransferases. The researchers interpret this as evidence that these enzymes are not essential in aquatic habitats, where constant water immersion buffers cells against the osmotic fluctuations that terrestrial organisms must endure. Blastocladiomycota, which are motile but have colonized semi-terrestrial niches, emerge as an evolutionary bridge, retaining ancestral fungal traits while also displaying innovations typical of the Dikarya.

The study also uncovered a remarkable temporal signature in the molecular clocks of key enzymes. By constructing maximum likelihood phylogenetic trees with IQ-TREE and calibrating them with least squares dating using established divergence times for the major fungal lineages, the researchers traced when specific gene duplications occurred. Duplications of acid sphingomyelin phosphodiesterase and UDP-glucuronosyltransferase in non-flagellated fungi cluster around 200 to 300 million years ago, close to the estimated period of fungal terrestrialization, which is exemplified by the famous Rhynie chert fossils from Scotland dated to approximately 410 million years ago. In Glomeromycota and Dikarya, however, the divergence of acid sphingomyelin phosphodiesterase coincides instead with the evolutionary radiation of flowering plants around 120 million years ago, suggesting a second wave of sphingolipid innovation tied to the rise of the mycorrhizal partnerships that dominate terrestrial ecosystems today.

The ceramide synthase family, which catalyzes the pivotal acylation step in ceramide production, tells its own evolutionary story. The enzyme is not only conserved across all fungi but has undergone multiple independent expansions in vertebrates and in distinct fungal phyla, including Mortierellomycota, filamentous Dikarya, and Entomophthoromycota. Phylogenetically, ceramide synthases split into an animal-like clade containing all CERS1-6 reference sequences from animals, plants, and flagellated fungi, and separate fungal-specific clades that include the Saccharomyces cerevisiae paralogs LAG1 and LAC1. Some paralogs have been recruited for entirely new purposes, such as the sphingosine N-acyltransferase-like proteins FUM17 and ALT7 found in Gibberella moniliformis and Alternaria alternata, which are implicated in mycotoxin biosynthesis rather than membrane construction.

Beyond the evolutionary narrative, the study carries significant biotechnological and medical implications. Ceramide synthase has recently been identified as a potential antifungal drug target, and its deletion in pathogenic fungi abolishes virulence. Transcriptomic data from the human pathogen Rhizopus delemar reveal that during infection of human airway epithelial cells, the fungus downregulates de novo ceramide synthesis while upregulating enzymes involved in sphingomyelin catabolism and ceramide recycling, suggesting a metabolic shift toward ceramide recovery that supports pathogenicity. Similarly, the oleaginous yeast Yarrowia lipolytica carries multiple copies of acid sphingomyelin phosphodiesterase, potentially linked to its remarkable lipid-producing capacity, a trait of growing interest for industrial biotechnology.

The researchers also examined publicly available transcriptomes to verify that the genes they identified are actually active. In axenic cultures of Mucoromycota and Mortierellomycota, most sphingolipid metabolism genes show expression, with patterns differing between species and environmental conditions. Under anaerobic conditions, the anaerobic gut symbiont Smittium and the parasite Entomophthora muscae show distinct expression profiles, while in the mycorrhizal fungus Rhizophagus irregularis, association with host plants triggers upregulation of specific desaturases and glycosyltransferases. These expression patterns confirm that sphingolipid metabolism is not a static inheritance from deep evolutionary time but a dynamic system that fungi actively tune in response to their surroundings, whether those surroundings are a mammalian lung, a plant root, or the oxygen-poor interior of a herbivore gut.

Subject of Research: Evolutionary diversity of sphingolipid metabolism proteins across the fungal tree of life

Article Title: Evolutionary diversity of sphingolipid metabolism proteins in fungi

Article References: Płecha, M., Sokołowska, B., Barua, D., Bartczak, J., Sobczyk, M., Koperska, D., Kułakowska, A., Komosa, A., & Muszewska, A. (2026). Evolutionary diversity of sphingolipid metabolism proteins in fungi. IMA Fungus, 17, Article e177891. https://doi.org/10.3897/imafungus.17.177891

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.177891

Keywords: sphingolipids, ceramides, fungi, evolution, terrestrialization, membrane lipids, phylogenomics, Dikarya, flagellated fungi, molecular dating, sphingomyelin, glycosyltransferases

The story of Col-0 begins nearly a century ago in the European countryside. In the first half of the twentieth century, the German botanist Friedrich Laibach, who pioneered the use of Arabidopsis as a model organism, collected wild seeds near the city of Landsberg, a location that today corresponds to Gorzów in Poland. Among the material he gathered were the ancestors of what would eventually become one of the most important genetic resources in plant science. Laibach’s collections provided the raw stock from which later generations of researchers would select and stabilize the strains that now populate cold storage facilities and growth chambers across the globe.

The modern chapter of that story opened in the second half of the century, when George Rédei, a Hungarian-born geneticist who had moved to the United States, established his laboratory at the University of Missouri in Columbia. Working with material derived from the original collections, Rédei established the Arabidopsis line that took its name from its home city. He chose it deliberately: the Columbia line was stable and vigorous, qualities that made it ideal for the repetitive, demanding work of laboratory genetics. That decision, made on practical grounds, would echo through decades of plant biology, because Columbia-0 was ultimately selected as the very first plant genome to be sequenced, a landmark effort completed with its final publication in the year 2000.

From its humble beginnings as a wild plant gathered from the European countryside to its status as the laboratory workhorse of modern plant science, the history of Col-0 thus spans an entire century. During that century, the strain has been propagated in countless laboratories, passed between collaborators, deposited in stock centres, and redistributed to new generations of researchers. Each transfer and each round of seed multiplication represents an opportunity for change: a DNA replication error here, a spontaneous mutation there, a shift in the pattern of chemical tags that decorate the genome and silence or activate genes without altering the underlying sequence.

To understand just how much change has accumulated, the new study took an unusually comprehensive approach. The researchers assembled 78 supposedly identical Col-0 strains obtained from various laboratories and stock centres around the world, each with a documented propagation history. For every strain, they performed whole-genome sequencing and methylome sequencing, the latter revealing the distribution of methyl groups across the DNA, the primary form of epigenetic modification in plants. This dual strategy allowed them to locate both genetic mutations, which alter the sequence of DNA letters, and epimutations, which alter the pattern of methylation while leaving the sequence intact. For a selected subset of lines, the team added a transcriptome analysis, examining how the accumulated differences translated into changes in gene activity.

The results were striking in their detail. Reminiscent of earlier studies on the accumulation of genetic changes in natural populations, the analysis identified many single-nucleotide polymorphisms across the collection of supposedly identical strains. These were not limited to silent changes in non-coding regions: the researchers found non-synonymous substitutions that alter the amino acid sequences of proteins, and in some cases high-impact mutations affecting gene start or stop codons, the signals that define where a gene begins and ends. Such mutations have the potential to truncate or extend proteins dramatically, and their presence in laboratory strains demonstrates that even the most carefully maintained genetic resources are not frozen in time.

Intriguingly, however, these high-impact variants appeared at a lower rate than would be expected by chance. The most likely explanation, the researchers suggest, is a form of purifying selection imposed not by nature but by researchers themselves over the years. Lines of Col-0 that show obvious phenotypic divergence, such as altered growth, development, or morphology, are generally discarded by observant scientists who recognize that something has gone wrong with their stock. This ongoing, largely unintentional culling acts as a filter, removing the most damaging mutations before they can spread through the community. What remains, and what quietly accumulates instead, are the small-effect mutations and epimutations that do not produce conspicuous symptoms.

That is precisely where the danger lies for experimental reproducibility. Small-effect changes can slowly build up in a lineage and, over many generations, end up subtly modifying phenotypes in ways that are difficult to detect by eye but large enough to influence experimental outcomes. A gene whose expression differs slightly between two laboratories’ Col-0 stocks could alter a plant’s response to stress, its flowering time, or its immune reactions, confounding comparisons between results obtained in different places. The study’s methylome data show that epigenetic variation, which can arise and be inherited far more readily than DNA sequence changes, adds a further layer of divergence that standard genotyping would entirely miss.

Perhaps the most remarkable result of the analysis is its reconstruction of the strain’s genealogy. Using molecular dating and a calibrated genetic lineage reconstruction based on both genetic and epigenetic changes, the researchers traced the relationships among the 78 strains back to a most recent common ancestor living roughly 55 to 60 generations ago. That timescale corresponds almost exactly to about one generation per year since the establishment of the Columbia dynasty, a rate that matches the practical tempo of laboratory propagation, in which seeds are typically multiplied and passaged on an annual cycle. In effect, the family tree of Col-0 written in its genomes recapitulates the written history of its distribution, a striking convergence of molecular and documentary records.

The broader lesson extends well beyond Arabidopsis. Col-0 was chosen as the first plant genome to be sequenced precisely because it was assumed to be a stable, uniform reference, and it has served that role for more than two decades. But the new findings demonstrate that the notion of a single canonical Col-0 is an idealization. Every vial of seeds in every stock centre represents a snapshot of a lineage that has been quietly evolving under laboratory conditions, shaped by drift, by methylation changes, and by the well-meaning but incomplete selection of the researchers who maintain it. For the plant science community, the practical message is clear: documenting strain provenance, periodically re-sequencing key stocks, and being transparent about which Col-0 derivative was used in any given study are no longer optional refinements but essential safeguards for reproducibility. For biology at large, the century-long story of Columbia-0 offers a vivid reminder that even our most cherished laboratory standards are living things, and that living things, given time, always change.

Subject of Research: Genetic and epigenetic divergence among laboratory strains of the Arabidopsis thaliana reference line Columbia-0 (Col-0)

Article Title: Col-0 genetic divergence

Article References: Tena, G. (2026). Col-0 genetic divergence. Nature Plants, 12(9), 1658-1658. https://doi.org/10.1038/s41477-026-02417-2

Image Credits: AI Generated

DOI: 10.1038/s41477-026-02417-2

Keywords: Arabidopsis thaliana, Col-0, genome sequencing, methylome, epimutations, single-nucleotide polymorphisms, purifying selection, plant genetics, laboratory strains, reproducibility, molecular dating, transcriptome