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Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants remains poorly understood. Allopolyploidy, where post-hybridization genome doubling merges parental genomes that may differ markedly in chromosomal architecture, has the potential to increase centromeric complexity and influence genomic plasticity. We explore this possibility in carnivorous Caryophyllales, a morphologically and chromosomally diverse plant lineage encompassing sundews, Venus flytraps, and Nepenthes pitcher plants. Focusing on sundews (Drosera), we generated chromosome-scale assemblies of holocentric D. regia and monocentric D. capensis, which share an allohexaploid origin but have diverged dramatically in genome structure. D. regia retains ancestral chromosomal fusions, dispersed centromeric repeats, and conserved synteny, whereas D. capensis exhibits extensive chromosomal reorganization and regionally localized centromeres after a lineage-specific genome duplication. Phylogenomic evidence traces D. regia to an ancient hybridization between sundew- and Venus flytrap-like ancestors, setting it apart within its infrageneric context. Genus-wide satellite DNA repeat profiling reveals rapid turnover and species-level variation in centromere organization. Together, these results establish sundews as a natural system for investigating how centromere dynamics interact with recurrent polyploidization and episodes of ecological innovation to shape genomic resilience. 

Abstract Cases of convergent adaptation, especially between close relatives within a lineage, provide insights into constraints underlying the mechanisms of evolution. We examined this in the carnivorous plant family Lentibulariaceae, with its highly divergent trap designs but shared need for prey digestion, by generating a chromosome-level genome assembly for Pinguicula gigantea, the giant butterwort. Our work confirms a history of whole-genome duplication in the genus and provides strong phylogenomic evidence for a sister-group relationship between Lentibulariaceae and Acanthaceae. The genome also reveals that a key digestive adaptation, the expansion of cysteine protease genes active in digestion, was achieved through independent tandem duplications in the butterwort (Pinguicula) and its close relative, the bladderwort (Utricularia). Most of these parallel expansions arose in non-homologous regions of the two genomes, with a smaller subset located on homologous blocks. This study provides clear genomic evidence for convergent evolution and illustrates how similar selective pressures can repeatedly shape genomes in analogous ways. 

Despite growing interest in beyond-group symmetries in quantum condensed matter systems, there are relatively few microscopic lattice models explicitly realizing these symmetries, and many phenomena have yet to be studied at the microscopic level. We introduce a one-dimensional stabilizer Hamiltonian composed of group-based Pauli operators whose ground state is a $G\times \mathrm{Rep}\left(G\right)$-symmetric state: the $G$-cluster state introduced by Brell []. We show that this state lies in a symmetry-protected topological (SPT) phase protected by $G\times \mathrm{Rep}\left(G\right)$symmetry, distinct from the symmetric product state by a duality argument. We identify several signatures of SPT order, namely, protected edge modes, string order parameters, and topological response. We discuss how $G$-cluster states may be used as a universal resource for measurement-based quantum computation, explicitly working out the case where $G$is a semidirect product of Abelian groups. Published by the American Physical Society2025 

Abstract Living in nutrient-poor environments, the carnivorous Venus flytrapDionaea muscipulacaptures 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. TheDionaea muscipulaDYSCALCULIA (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 DYSC’s delayed trap movement, we generated a chromosome-scaleDionaeagenome 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. 

Abstract Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use 5 leaves to evaluate admixture. Among these, the DFOIL method, which tests allelic patterns on the “symmetric” tree S = (((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the “asymmetric” tree A = ((((1,2),3),4),5) and the “quasisymmetric” tree Q = (((1,2),3),(4,5)), which can considerably supplement the “symmetric“ S = (((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality. Code and documentation available at https://github.com/KalleLeppala/Delta-statistics. 

The CSS code construction is a powerful framework used to express features of a quantum code in terms of a pair of underlying classical codes. Its subsystem extension allows for similar expressions, but the general case has not been fully explored. Extending previous work of Aly, Klappenecker, and Sarvepalli \cite{AKS06}, we determine subsystem CSS code parameters, express codewords, and develop a Steane-type decoder using only data from the two underlying classical codes. Generalizing a result of Kovalev and Pryadko \cite{KP13}, we show that any subsystem stabilizer code can be doubled to yield a subsystem CSS code with twice the number of physical, logical, and gauge qudits and up to twice the code distance. This mapping preserves locality and is tighter than the Majorana-based mapping of Bravyi, Terhal, and Leemhuis \cite{BTL10}. Using Goursat's Lemma, we show that every subsystem stabilizer code can be constructed from two nested subsystem CSS codes satisfying certain constraints, and we characterize subsystem stabilizer codes based on the nested codes' properties. 

As with classical computers, quantum computers require error-correction schemes to reliably perform useful large-scale calculations. The nature and frequency of errors depends on the quantum computing platform, and although there is a large literature on qubit-based coding, these are often not directly applicable to devices that store information in bosonic systems such as photonic resonators. Here, we introduce a framework for constructing quantum codes defined on spheres by recasting such codes as quantum analogues of the classical spherical codes. We apply this framework to bosonic coding, and we obtain multimode extensions of the cat codes that can outperform previous constructions but require a similar type of overhead. Our polytope-based cat codes consist of sets of points with large separation that, at the same time, form averaging sets known as spherical designs. We also recast concatenations of Calderbank–Shor–Steane codes with cat codes as quantum spherical codes, which establishes a method to autonomously protect against dephasing noise. 

Abstract The inversion of C3 stereochemistry in monoterpenoid indole alkaloids (MIAs), derived from the central precursor strictosidine (3S), is essential for synthesizing numerous 3RMIAs and oxindoles, including the antihypertensive drug reserpine found inRauvolfia serpentina(Indian snakeroot) andRauvolfia tetraphylla(devil pepper) of the plant family Apocynaceae. MIA biosynthesis begins with the reduction of strictosidine aglycone by various reductases, preserving the initial 3Sstereochemistry. In this study, we identify and biochemically characterize a conserved oxidase-reductase pair from the Apocynaceae, Rubiaceae, and Gelsemiaceae families of the order Gentianales: the heteroyohimbine/yohimbine/corynanthe C3-oxidase (HYC3O) and C3-reductase (HYC3R). These enzymes collaboratively invert the 3Sstereochemistry to 3Racross a range of substrates, resolving the long-standing question about the origin of 3RMIAs and oxindole derivatives, and facilitation of reserpine biosynthesis. Notably,HYC3OandHYC3Rare located within gene clusters in both theR. tetraphyllaandCatharanthus roseus(Madagascar periwinkle) genomes, which are partially homologous to an elusive geissoschizine synthase (GS) gene cluster we also identified in these species. InR. tetraphylla, these clusters occur closely in tandem on a single chromosome, likely stemming from a single segmental duplication event, while inC. roseus, a closely related member of rauvolfioid Apocynaceae, they were later separated by a chromosomal translocation. The ancestral genomic context for both clusters can be traced all the way back to common ancestry with grapevine. Given the presence of syntenic GS homologs inMitragyna speciosa(Rubiaceae), the GS cluster, at least in part, probably evolved at the base of the Gentianales, which split from other core eudicots up to 135 million years ago. We also show that the strictosidine biosynthetic gene cluster, required to initiate the MIA pathway, plausibly evolved concurrently. The reserpine biosynthetic cluster likely arose much later in the rauvolfioid lineage of Apocynaceae. Collectively, our work uncovers the genomic and biochemical basis for key events in MIA evolution and diversification, providing insights beyond the well-characterized vinblastine and ajmaline biosynthetic pathways. 

Shadow tomography is a framework for constructing succinct descriptions of quantum states using randomized measurement bases, called “classical shadows,” with powerful methods to bound the estimators used. We recast existing experimental protocols for continuous-variable quantum state tomography in the classical-shadow framework, obtaining rigorous bounds on the number of independent measurements needed for estimating density matrices from these protocols. We analyze the efficiency of homodyne, heterodyne, photon-number-resolving, and photon-parity protocols. To reach a desired precision on the classical shadow of an N-photon density matrix with high probability, we show that homodyne detection requires order O(N4+1/3) measurements in the worst case, whereas photon-number-resolving and photon-parity detection require O(N4) measurements in the worst case (both up to logarithmic corrections). We benchmark these results against numerical simulation as well as experimental data from optical homodyne experiments. We find that numerical and experimental analyses of homodyne tomography match closely with our theoretical predictions. We extend our single-mode results to an efficient construction of multimode shadows based on local measurements. 

We generalize the notion of quantum state designs to infinite-dimensional spaces. We first prove that, under the definition of continuous-variable (CV) state t-designs from [Blume-Kohout et al., Commun.Math. Phys. 326, 755 (2014)], no state designs exist for t ≥ 2. Similarly, we prove that no CV unitary t-designs exist for t ≥ 2. We propose an alternative definition for CV state designs, which we call rigged t-designs, and provide explicit constructions for t ¼ 2. As an application of rigged designs, we develop a design-based shadow-tomography protocol for CV states. Using energy-constrained versions of rigged designs, we define an average fidelity for CV quantum channels and relate this fidelity to the CV entanglement fidelity. As an additional result of independent interest, we establish a connection between torus 2-designs and complete sets of mutually unbiased bases.