Biology subjects

Kirshner, J.

Publications and source records attributed to Kirshner, J..

4 recordsLinked to original sources

bioRxiv2025

Genome evolution and convergent innovation in the carnivorous plant Sarracenia purpurea

The repeated evolution of certain complex traits raises a fundamental question of how genomes generate ecological novelty while preserving developmental stability. Carnivorous pitcher plants, which modify a core organ of plant performance, the leaf, exemplify this challenge, yet the genomic basis of their convergent evolution has not been resolved. We present a chromosome-scale genome assembly for Sarracenia purpurea and analyze it alongside eight additional angiosperms spanning its parent clade Ericales and several other carnivorous lineages. The genome reveals extensive syntenic duplicate blocks arising from ancient polyploidy events, with diffuse, alternating dominant and recessive segments interleaved along chromosomes. Dominant regions are biased toward retained copies of dosage-sensitive regulatory genes, including AGO1, BRX, GATA11, ETC1 and RCD1. These genes highlight a conserved regulatory scaffold associated with leaf morphogenesis, including epidermal differentiation, auxin-mediated patterning, and redox-integrated coordination. By contrast, tandem gene duplications preferentially accumulate in structurally labile genomic regions and constitute a complementary, rapidly evolving component of the genome, enriched for ecological effector functions, including detoxification, glutathione-mediated redox buffering, antifungal pathways, and cuticle modification activities. Comparative union-based functional analyses across four carnivorous taxa reveal convergent recruitment of oxidative, transport, microbial-interaction, and cell-wall processes during independent trap evolution. Transcriptomic data confirm consistent activation of these pathways in pitchers. These findings demonstrate that complex traits arise through a genome-wide partitioning between polyploidy-derived, conserved developmental regulation and tandem-driven ecological specialization, here partitioning leaf architectural control from rapidly evolving functions associated with pitfall-based prey capture.

genomics↗

bioRxiv2025

Impaired trap closure in the counting-deficient Venus flytrap mutant DYSCALCULIA is caused by cell wall biomechanics

Living in nutrient-poor environments, the carnivorous Venus flytrap Dionaea muscipula captures animal prey to compensate for this deficiency. Stimulation of trigger hairs located on the inner trap surface elicits an action potential (AP). While two consecutive APs result in fast trap closure in wildtype (WT) plants, sustained AP generation by the insect struggling to escape the trap leads to jasmonic acid (JA) biosynthesis, formation of the digestive "stomach", and release of enzymes needed to decompose the victim. The Dionaea muscipula DYSCALCULIA (DYSC) mutant is able to fire touch-induced APs, but unlike WT plants, it does not snap-close its traps after two consecutive APs. Moreover, DYSC plants fail to properly initiate the JA pathway in response to mechanostimulation and even wounding, a well-known JA-dependent process conserved among plants. As demonstrated in previous studies, this DYSC mutant defect is associated with impaired decoding of mechanostimulation (i.e. touch) -induced Ca2+ signals. External JA application to the trap, however, restores slow trap closure and digestive gland function in DYSC, while rapid trap closure is JA-independent and cannot be rescued by exogenous JA application. Higher frequency mechanostimulation and thus more APs, however, revealed that DYSC is still able to close its traps, albeit much slower than WT plants. To reveal the molecular underpinnings of DYSCs delayed trap movement, we generated a chromosome-scale Dionaea genome assembly and profiled gene expression. The refined transcriptomic analysis uncovered widespread misregulation of cell wall-related genes in DYSC, implicating altered cell wall plasticity in the sluggish mutant. Cell indentation studies by atomic force microscopy revealed a strictly localized and strikingly enhanced stiffening of the cell wall for DYSC that may hinder rapid trap closure and snap buckling. Together, these genomic, transcriptomic, and biophysical data identify cell wall elasticity as a key constraint on voltage and Ca2+ dependent trap kinetics. This finding documents the interrelationship between mechanosensing and Ca2+ signaling in the ultrafast capture organ of the Venus flytrap.

plant biology↗

bioRxiv2025

Ancient gene clusters initiate monoterpene indole alkaloid biosynthesis and C-3 stereochemistry inversion

The inversion of C3 stereochemistry in monoterpenoid indole alkaloids (MIAs), derived from the central precursor strictosidine (3S), is a critical step for the biosynthesis of numerous 3R MIAs and spirooxindoles, including the antihypertensive drug reserpine. While early MIA biosynthesis preserves the 3S configuration, the mechanism underlying C3 inversion has remained unresolved. Here, we identify and biochemically characterize a conserved oxidase-reductase pair in the Gentianales order: the heteroyohimbine/yohimbine/corynanthe C3-oxidase (HYC3O) and C3-reductase (HYC3R), which together invert the 3S stereochemistry to 3R across diverse substrates. Notably, HYC3O and HYC3R reside in gene clusters in Rauvolfia tetraphylla and Catharanthus roseus, homologous to an elusive geissoschizine synthase (GS) cluster we also uncovered. In R. tetraphylla, these clusters are in tandem on a single chromosome, likely derived from segmental duplication, whereas in C. roseus they reside on separate chromosomes due to translocation. Comparative genomics indicate the GS cluster originated at the base of Gentianales ([~]135 Mya), coinciding with the evolution of the strictosidine synthase cluster, while the reserpine cluster arose later in rauvolfioid Apocynaceae. Together, these findings uncover the genomic and biochemical basis for key events in MIA evolution and diversification, providing insights beyond the canonical vinblastine and ajmaline biosynthetic pathways.

biochemistry↗

bioRxiv2024

Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale

Exploring a species paleohistory is crucial for understanding its responsiveness to climatic events, identifying drivers of adaptation, and developing effective biodiversity conservation strategies in the face of ongoing climate change. We analyzed 200 genomes of the perennial herb woodland strawberry (Fragaria vesca L.) from across Europe and investigated the population structure and demographic history of the species during past geoclimatic events. We found a clear division of populations into western and eastern genetic clusters, indicative of distinct glacial refugia and adaptations to variation in temperature seasonality. The eastern core populations were several times larger (defined as effective population size, NE) than populations in other regions, showed no evidence of inbreeding, and were resilient to several glacial maxima. However, we observed decreasing NE and higher inbreeding in populations toward range edges, particularly in the north, where these individuals went through bottlenecks during glaciations. Population divergence suggested that western and eastern Europe were colonized from separate refugia in multiple waves during the Holocene, while the largest current populations from the northern Mediterranean to southern regions of the Nordic countries formed a connected population chain with gene flow between eastern core populations and western Europe, primarily occurring through Central Europe. Similar patterns of colonization and hybridization may have occurred during past interglacial periods, contributing to the present-day population structure of woodland strawberry. We suggest that the unprecedented resolution of the species climatic history across six glacial-interglacial cycles presented here holds the promise of transforming the general understanding of species paleohistory through geoclimatically tracing ancestral haplotypes.

plant biology↗