Cyclins are the metronomes of cell division. By binding and activating cyclin-dependent kinases, they usher cells through the checkpoints of the cell cycle, and their influence extends well beyond mitosis into flowering, meristem formation, seed development, and morphogenesis. Previous work in Arabidopsis thaliana had shown that disabling the CYCD3 family delays flowering under standard conditions, while studies in snapdragon demonstrated that D-type cyclins are expressed in precisely the developmental zones where floral organs take shape. Yet despite decades of functional work, the question of how cyclin gene families expand and diversify across whole lineages—especially in polyploid crops—remained largely unanswered. The new analysis, led by Aldrin Y. Cantila and colleagues, was designed to close that gap by treating cyclin evolution as a comparative genomic problem across the entire Brassicaceae family.

The scale of the undertaking is itself notable. The team used 49 well-characterized Arabidopsis cyclin proteins as reference queries and screened ten published genomes using BLASTp with stringent significance thresholds, then validated every candidate through Hidden Markov Model searches against the Pfam protein family database. In the Brassica species, an additional layer of rigor was applied: each putative cyclin was subjected to reciprocal BLASTp against the Arabidopsis proteome, and only sequences that returned the original Arabidopsis cyclins as their top hits were accepted as true homologs. After domain confirmation, 1,087 proteins representing 23 distinct cyclin types stood as the definitive set. A-type and D-type cyclins dominated the census, with 241 and 225 genes respectively, followed by B-type (213), U-type (164), and T-type (112) cyclins. The D-type family proved especially diverse, splitting into seven subtypes with cycD3 alone contributing 78 genes across the ten species.

The numbers tell a striking story about ploidy. The six diploid species in the sample—including B. rapa, B. nigra, B. oleracea, and three Arabidopsis species—averaged 71.5 cyclin genes each, while the four allotetraploids—B. napus, B. juncea, B. carinata, and A. suecica—averaged 164.5, ranging as high as 189 in canola itself. To understand where all these extra copies came from, the researchers deployed DupGen_finder, a computational tool that classifies duplicated gene pairs into five mechanistic categories: tandem, proximal, transposed, dispersed, and whole-genome duplication (WGD). Across all ten genomes they catalogued 1,845 duplication events involving 1,063 cyclin genes, and the dominant mechanism was unambiguous. Of the total, 969 events—more than half—were classified as WGD, the fossil record of ancient genome doubling preserved in chromosomal collinearity.

The Brassica species carried by far the heaviest duplication burden, with B. juncea recording 377 events involving 185 genes and B. napus close behind at 372 events involving 186 genes. In both of these allotetraploids, WGD accounted for 68 percent of all duplication events. By contrast, Arabidopsis species averaged only 90.3 duplication events, and thale cress—whose lineage never experienced the whole-genome triplication that shaped the Brassica genus—showed WGD contributions as low as 22 percent. The authors attribute the Brassica expansion primarily to the lineage-specific whole-genome triplication event documented in earlier sequencing work, which multiplied gene copy numbers three- to six-fold relative to Arabidopsis before subsequent fractionation and differential gene loss sculpted the modern complement. In the allotetraploids, the picture grows more complex still: within B. napus, the team identified 149 intra-genomic duplications occurring within the A and C subgenomes and 214 inter-genomic duplications spanning subgenomes, the molecular signature of the extensive chromosome reshuffling and homoeologous exchange that followed hybridization of the two diploid progenitors.

Orthology analysis added a genealogy to this architecture. Using OrthoFinder, the researchers traced 852 one-to-one orthologous pairs linking cyclin genes in diploid progenitors to their descendants in allotetraploid species, involving 366 genes in total. In B. napus, orthologs inherited from B. rapa showed 67.7 percent retention on the expected A subgenome, with the remaining third exchanged onto the C subgenome; orthologs from B. oleracea showed 68.8 percent retention on the C subgenome. Retention rates across all progenitor-allotetraploid combinations ranged from 66.6 percent to 87.5 percent, with B. nigra orthologs showing the tightest fidelity in B. juncea. This conservation—most orthologs staying put on their ancestral subgenomes while a minority migrate—supports the gene balance hypothesis, which holds that dosage-sensitive genes embedded in protein interaction networks are preferentially retained in stoichiometric proportions, because disruption of copy number can destabilize cellular machinery.

Beyond raw counts, physical organization revealed another layer of complexity. The team identified 120 cyclin gene clusters across the ten genomes, comprising 263 genes, where clusters were defined as two or more cyclin genes within a 200-kilobase window on the same chromosome. Eighty-eight of these clusters were homogeneous, containing genes of a single cyclin type and likely arising through tandem duplication, while 32 were heterogeneous mixtures of different types, products of segmental duplication, ectopic recombination, or transposition. The allotetraploids again led the tally: A. suecica hosted 22 clusters, and B. juncea, B. carinata, and B. napus each carried 19 or 20. Whether such clustering facilitates coordinated transcriptional regulation or simply represents genomic debris of ancient amplification remains an open question, but the pattern mirrors findings in other large gene families such as plant disease resistance genes.

Phylogenetic reconstruction confirmed deep evolutionary conservation. Aligning 1,079 nonredundant cyclin protein sequences and building a maximum-likelihood tree with IQ-TREE under the best-fit Q.PFAM+R3 substitution model, supported by 1,000 ultrafast bootstrap replicates, the analysis resolved three major clades whose compositions match the canonical cyclin classification established across land plants. Clade 1 gathered the seven D-type families together with cycA1; Clade 2, the largest with 401 members, united cycA2 with the B-type cyclins and several minor types; and Clade 3 contained the T-, U-, A3-, H-, and L-type cyclins in a heterogeneous assemblage. This architecture indicates that the major cyclin lineages originated early in plant evolution and have retained their functional identities even as duplication multiplied their members.

The bridge from evolutionary genomics to agronomy came when the researchers cross-referenced their cyclin inventory against flowering-time quantitative trait loci in B. napus. Compiling 174 SNPs previously linked to flowering time from genome-wide association studies using the Brassica 60K Illumina array, they delineated QTL intervals with a 50-kilobase sliding window—a threshold justified by published linkage disequilibrium decay estimates for canola, which show genome-wide half-decay below 45 kilobases. Five cyclin genes fell within these intervals. The team then turned to a pan-genomic comparison, BLASTp-querying the protein sequences of these five candidates against eight fully sequenced B. napus cultivars spanning early (Westar, No2127), intermediate (Gangan, Shengli, ZS11, Zheyou7), and late (Quinta, Tapidor) flowering phenotypes.

Two candidates stood out. In Bna21cycA2, both early-flowering cultivars carry a phenylalanine at amino acid position 411 where all other genomes carry a threonine; in Bna113cycD4, the early group shares a valine at position 100 where the rest carry a leucine. In neighbor-joining phylogenies built from the homologous protein alignments, Westar and No2127 consistently grouped together in the same clade for both genes—a pattern not observed in the other cultivars. The intermediate-flowering genotypes carried their own distinctive variants at other positions. The authors are careful to note that these amino acid polymorphisms are putative candidates whose causal role in flowering-time regulation requires validation through genetic mapping or functional studies, but the consistency of the pattern across independent genomes makes the two genes attractive targets for molecular marker development aimed at tailoring flowering behavior.

Taken together, the study delivers a dual contribution: a definitive evolutionary account of how polyploidization sculpted the cyclin repertoire of one of botany’s most economically important families, and a shortlist of candidate loci that connect cell-cycle machinery to a trait that governs yield stability and environmental adaptation. As the authors note, the finding that cyclins participate in broader developmental networks beyond their classical cell-cycle roles suggests that manipulating these genes could offer breeders a lever for controlling reproductive timing in Brassicaceae crops. In an era when climate variability makes precise flowering control increasingly valuable for canola and vegetable brassicas, the humble cyclin—long the province of cell biologists—may be about to enter the breeder’s toolkit.

Butterfly lilies in the genus Wachendorfia produce flowers with a striking form of asymmetry. On each plant, every flower develops with its female reproductive structure, known as the style, pointing either to the left or to the right. The central male structure, the stamen, bends in the opposite direction. A plant therefore carries flowers with a consistent “handedness,” creating mirror-image forms that resemble the left and right versions of a glove.

This unusual arrangement has important consequences for reproduction. Because the style and stamen point in opposite directions, pollen is less likely to be transferred directly from a flower’s anthers to its own stigma. Instead, pollinators moving between plants with opposite floral orientations are more likely to pick up pollen from one form and deposit it on the corresponding reproductive structure of the other. The arrangement therefore reduces self-pollination and encourages pollen exchange between genetically distinct individuals.

The evolutionary puzzle attracted the attention of Charles Darwin late in his life. In a letter written just nine days before his death, Darwin discussed the curious left-right differences observed in flowers. More than a century later, an international team involving researchers from the University of Cape Town, the University of Potsdam and Wageningen University has traced the phenomenon to a genetic region that functions as a developmental control system.

The researchers compared DNA from hundreds of left- and right-oriented plants representing four Wachendorfia species and the related species Barberetta aurea. Their analysis identified a segment of DNA present only in plants that develop right-oriented flowers. The region contains two closely linked genes, YUC-R and miR156, which together act as a supergene-like switch. A supergene is a group of neighboring genes inherited together because genetic recombination between them is suppressed or limited, allowing several coordinated traits to evolve as a single functional unit.

The two genes influence different aspects of floral development. YUC-R belongs to the YUCCA family of genes, which participate in the production of auxin, a plant hormone that regulates cell expansion, tissue growth and directional development. Changes in auxin distribution can cause one side of a developing organ to grow faster than the other, producing curvature. In butterfly lilies, the activity of YUC-R helps establish the bending direction of the central stamen.

The second gene, miR156, produces a small regulatory RNA molecule rather than a conventional protein. MicroRNAs control gene activity by binding to messenger RNAs and preventing them from being translated into proteins or promoting their degradation. The butterfly lily version of miR156 was shown by University of Cape Town honours students Oliver Marketos and Anand Shankar to perform a regulatory role comparable to that of the gene in the laboratory plant Arabidopsis thaliana. In the flower, its activity helps determine the direction taken by the style.

Natural mutants provided an especially powerful test of the genetic model. During a search across the Western Cape, the team located plants carrying naturally occurring defects in the two genes. When YUC-R was disrupted, the stamen bent in the opposite direction from normal. When miR156 was defective, the style switched orientation. These contrasting effects demonstrated that the genes control separate but coordinated components of the flower’s mirror-image architecture.

The work also revealed that genes are not acting alone. While observing developing flower buds, Professor Nicola Illing accidentally positioned one bud upside down. MSc student Caroline Robertson noticed that the flower did not simply continue its original developmental trajectory. Instead, its style and stamen reversed orientation. Further observations indicated that gravity provides a directional signal during the brief developmental window when the flower establishes its handedness. The result suggests that the genetic switch determines how the plant responds to its surroundings, while gravity helps define the direction in which the response unfolds.

Obtaining the genetic evidence required overcoming a practical obstacle. Butterfly lily tissues contain high concentrations of sticky carbohydrates that interfere with the purification of DNA and RNA, making molecular analysis difficult. During her MSc research, Kelly Shepherd developed a method for extracting high-quality genetic material from young flower buds. That protocol enabled the team to sequence and compare the genomes and gene activity patterns needed to identify the handedness region. The combined genetic, developmental and ecological evidence now provides a detailed explanation for how these plants break left-right symmetry.

The discovery extends beyond butterfly lilies. Left-right asymmetry is a fundamental problem in developmental biology, appearing in organisms ranging from humans to flowering plants. In animals, internal organs can be positioned asymmetrically even when the external body plan is broadly symmetrical. In plants, asymmetry may arise through unequal growth, hormone transport, cell division or environmental sensing. The butterfly lily system offers an unusually clear example in which a small genetic region, hormone-linked growth, microRNA regulation and gravity interact to produce a visible evolutionary trait.

The findings may also help explain how mirror-image flowers evolve and persist in natural populations. Wachendorfia species are found in South Africa’s Western and Eastern Cape, while Barberetta aurea occurs in KwaZulu-Natal and the Eastern Cape. The marsh butterfly lily, Wachendorfia thyrsiflora, grows near streams and is cultivated in botanical gardens worldwide. Other species, including W. brachyandra, W. multiflora and W. paniculata, flower across the Western Cape from the Cederberg to Cape Agulhas, generally between August and November. As these plants enter bloom, their apparently delicate mirror-image flowers will display the outcome of a precisely coordinated genetic and environmental decision made early in development.

Subject of Research: Plant developmental biology and evolutionary biology

Article Title: Supergene control of chiral development in mirror-image flowers

News Publication Date: 30-Jul-2026

Web References: Science article; Charles Darwin letter; University of Cape Town Department of Molecular and Cell Biology

References: Science. DOI: 10.1126/science.aeb1157

Image Credits: Nicola Illing

Keywords: butterfly lilies, Wachendorfia, Barberetta aurea, floral asymmetry, left-right symmetry, flower development, supergene, YUC-R, miR156, auxin, microRNA, gravity, plant evolution, developmental biology

The focal point of this investigation is a gene known as RLF, part of a gene family that had been implicated primarily in the lateral root formation of Arabidopsis thaliana, a widely used model organism in plant biology. While the RLF gene’s influence on root emergence in Arabidopsis was established, its broader role across the plant kingdom had remained elusive. Fukaki’s team hypothesized that if this gene is fundamental to organ development, then its function might be conserved even in basal land plants such as liverworts, which diverged early in the evolution of terrestrial flora and lack many complex structures found in flowering plants.

To test this hypothesis, the team turned to Marchantia polymorpha, a species of liverwort that serves as a model organism for studying primitive land plants. Unlike vascular plants, liverworts do not possess true roots that facilitate water and nutrient uptake. Nevertheless, Marchantia harbors its own version of the RLF gene, providing a unique experimental system to explore gene function at an evolutionary baseline. The researchers employed advanced genetic manipulation techniques to knock out the RLF gene in liverworts and observed striking developmental abnormalities. The mutants exhibited severe distortions in multiple organ structures, underscoring that RLF is essential for maintaining normal organ morphology even in these primitive plants.

One of the most compelling aspects of the study was demonstrating that the RLF genes from Arabidopsis and Marchantia are functionally interchangeable. Through gene complementation experiments, the Arabidopsis RLF gene was able to substitute for its liverwort counterpart and vice versa. This cross-species functional equivalence implies a deep evolutionary conservation of molecular mechanisms governing organ development, reaching back hundreds of millions of years to the earliest land plants’ ancestors.

At the molecular level, the RLF gene encodes a protein classified within a large family of heme-binding proteins similar to cytochrome b5. Heme, an iron-containing porphyrin, is critical in numerous cellular processes, including electron transport and energy metabolism. Prior to this work, heme-binding proteins had not been associated with plant organogenesis, making this discovery a paradigm shift in understanding how metabolic cofactors can influence developmental pathways. Fukaki and colleagues confirmed that the RLF protein indeed carries heme in both liverwort and Arabidopsis contexts, suggesting a conserved biochemical function that transcends structural differences between plant lineages.

The evolutionary implications of this study extend beyond the functional discovery. Liverworts evolved long before vascular plants developed complex root systems, indicating that mechanisms facilitating organ development existed prior to the emergence of roots as specialized organs. Fukaki asserts that the co-option of the RLF gene represents a classic example of evolutionary innovation where pre-existing genetic modules are repurposed to enable new functions—in this case, the evolution of roots. This finding echoes a broader principle in evolutionary biology: new traits often arise through the modification of ancient genetic circuits rather than the invention of entirely novel genes.

Understanding how RLF operates within the intricate network of plant developmental signals remains a key objective. The research team anticipates that decoding the protein-protein interactions mediated by RLF and exploring its integration with hormonal pathways could unveil further insights into the molecular underpinnings of organogenesis. Such knowledge has the potential to transform agricultural science by enabling targeted manipulation of root and shoot architectures to improve crop resilience and nutrient uptake efficiency.

The research methodology hinged on combining genetic editing tools, comparative genomics, and phenotypic analyses. The use of Marchantia as a model organism was pivotal, leveraging its simplicity and genetic tractability to unravel biological questions that are challenging to address in more complex plants. By bridging findings from a basal land plant and a flowering plant, the study offers a compelling narrative of continuity and innovation in plant evolution.

Funded by several programs including Japan’s Ministry of Education (MEXT) and the Japan Society for the Promotion of Science, the project epitomizes international collaborative efforts, with contributing researchers from multiple Japanese institutions such as the University of Tokyo and Osaka University. This interdisciplinary and cooperative approach underscores the importance of merging developmental biology, evolutionary genomics, and biochemistry to tackle fundamental questions about life’s diversity.

In sum, this pioneering study by Kobe University scientists not only elucidates a previously unrecognized role for a heme-binding protein in plant organ development but also contributes a key piece to the evolutionary puzzle of how complex multicellular structures arose in terrestrial plants. The discovery reiterates that ancient genetic elements, refined and redeployed through evolutionary time, continue to shape the living world and may hold untapped potential for future scientific and agricultural breakthroughs.

Thanks to this novel insight into RLF’s conserved function, the scientific community gains a fresh perspective on the molecular continuity underlying life’s complexity. As FUKAKI Hidehiro remarks, the discovery that RLF has played an essential role since the dawn of land plants illuminates the intricate weaving of evolutionary history and molecular function, inspiring new research into plant development and evolution’s broader mechanisms.

Subject of Research: Not applicable

Article Title: Evolutionary conserved RLF, a cytochrome b5-like heme-binding protein, regulates organ development in Marchantia polymorpha

News Publication Date: 25-May-2025

Web References: DOI 10.1111/nph.70181

Image Credits: FUKAKI Hidehiro

Keywords: RLF gene, liverwort, Marchantia polymorpha, organ development, plant evolution, heme-binding protein, cytochrome b5-like protein, Arabidopsis thaliana, root development, evolutionary conservation, plant genetics, molecular evolution