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Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops., Two divergent haplotypes from a highly heterozygous lychee genome of the cultivar ‘Feizixiao’ and resequencing of 72 lychee accessions provide insights into the genome evolution and domestication history of lychee.

In arXiv:2110.06932, we argued that the chiral central charge -- a topologically protected quantity characterizing the edge theory of a gapped (2+1)-dimensional system -- can be extracted from the bulk by using an order parameter called the modular commutator. In this paper, we reveal general properties of the modular commutator and strengthen its relationship with the chiral central charge. First, we identify connections between the modular commutator and conditional mutual information, time reversal, and modular flow. Second, we prove, within the framework of the entanglement bootstrap program, that two topologically ordered media connected by a gapped domain wall must have the same modular commutator in their respective bulk. Third, we numerically calculate the value of the modular commutator for a bosonic lattice Laughlin state for finite sizes and extrapolate to the infinite-volume limit. The result of this extrapolation is consistent with the proposed formula up to an error of about 0.7%., 15+3 pages, 19 figures, Expanded version of arXiv:2110.06932

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000–115,000-year-old polar bear from the Svalbard Archipelago using a 10X coverage genome sequence and ten new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear’s lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 years. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published works. These findings may have implications for our understanding of climate change impacts: polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks, but also been the recipient of generalist, boreal genetic variants from brown bear during critical phases of Northern Hemisphere glacial oscillations.SignificanceInterspecific hybridization is a widespread phenomenon, but measuring its extent, directionality, and adaptive importance remains challenging. Ancient genomes, however, can help illuminate the history of modern organisms. Here, we present a genome retrieved from a 130,000–115,000-year-old polar bear and perform genome analyses of modern polar and brown bears throughout their geographic range. We find that the principal direction of ancient allele sharing was from brown bear into polar bear, although gene flow between them has likely been bidirectional. This inverts the current paradigm of unidirectional gene flow from polar into brown bear, and it suggests that polar bears were recipients of external genetic variation prior to their extensive population decline.

To survive in the nutrient-poor habitats, carnivorous plants capture small organisms comprising complex substances not suitable for immediate reuse. The traps of carnivorous plants, which are analogous to the digestive systems of animals, are equipped with mechanisms for the breakdown and absorption of nutrients. Such capabilities have been acquired convergently over the past tens of millions of years in multiple angiosperm lineages by modifying plant-specific organs including leaves. The epidermis of carnivorous trap leaves bears groups of specialized cells called glands, which acquire substances from their prey via digestion and absorption. The digestive glands of carnivorous plants secrete mucilage, pitcher fluids, acids, and proteins, including digestive enzymes. The same (or morphologically distinct) glands then absorb the released compounds via various membrane transport proteins or endocytosis. Thus, these glands function in a manner similar to animal cells that are physiologically important in the digestive system, such as the parietal cells of the stomach and intestinal epithelial cells. Yet, carnivorous plants are equipped with strategies that deal with or incorporate plant-specific features, such as cell walls, epidermal cuticles, and phytohormones. In this review, we provide a systematic perspective on the digestive and absorptive capacity of convergently evolved carnivorous plants, with an emphasis on the forms and functions of glands.

The Rabi model describes the simplest nontrivial interaction between a few-level system and a bosonic mode, featuring in multiple seemingly unrelated systems of importance to quantum science and technology. While exact expressions for the energies of this model and its few-mode extensions have been obtained, they involve roots of transcendental functions and are thus cumbersome and unintuitive. Utilizing the symmetric generalized rotating wave approximation (S-GRWA), we develop a family of approximations to the energies of the two-mode two-photon Rabi model. The simplest elements of the family are analytically tractable, providing good approximations in regimes of interest such as ultra- and deep-strong coupling. Higher-order approximate energies can be used if more accuracy is required., Comment: 7 pages, 2 figures; Accepted by Physics Letters A

Detection of weak forces and precise measurement of time are two of the many applications of quantum metrology to science and technology. We consider a quantum system initialized in a pure state and whose evolution is goverened by a Hamiltonian $H$; a measurement can later estimate the time $t$ for which the system has evolved. In this work, we introduce and study a fundamental trade-off which relates the amount by which noise reduces the accuracy of a quantum clock to the amount of information about the energy of the clock that leaks to the environment. Specifically, we consider an idealized scenario in which Alice prepares an initial pure state of the clock, allows the clock to evolve for a time $t$ that is not precisely known, and then transmits the clock through a noisy channel to Bob. The environment (Eve) receives any information that is lost. We prove that Bob's loss of quantum Fisher information (QFI) about $t$ is equal to Eve's gain of QFI about a complementary energy parameter. We also prove a more general trade-off that applies when Bob and Eve wish to estimate the values of parameters associated with two non-commuting observables. We derive the necessary and sufficient conditions for the accuracy of the clock to be unaffected by the noise. These are a subset of the Knill-Laflamme error-correction conditions; states satisfying these conditions are said to form a metrological code. We provide a scheme to construct metrological codes in the stabilizer formalism. We show that there are metrological codes that cannot be written as a quantum error-correcting code with similar distance in which the Hamiltonian acts as a logical operator, potentially offering new schemes for constructing states that do not lose any sensitivity upon application of a noisy channel. We discuss applications of our results to sensing using a many-body state subject to erasure or amplitude-damping noise., Comment: 102 pages (42+60), total 18 figures

ispartof: Cladistics vol:11 issue:2 pages:211-218 ispartof: location:United States status: published

In the carnivorous plant family Lentibulariaceae, the bladderwort lineage (Utricularia and Genlisea) is substantially more species-rich and morphologically divergent than its sister lineage, the butterworts (Pinguicula). Bladderworts have a relaxed body plan that has permitted the evolution of terrestrial, epiphytic, and aquatic forms that capture prey in intricately designed suction bladders or corkscrew-shaped lobster-pot traps. In contrast, the flypaper-trapping butterworts maintain vegetative structures typical of angiosperms. We found that bladderwort genomes evolve significantly faster across seven loci (the trnL intron, the second trnL exon, the trnL-F intergenic spacer, the rps16 intron, rbcL, coxI, and 5.8S rDNA) representing all three genomic compartments. Generation time differences did not show a significant association. We relate these findings to the contested speciation rate hypothesis, which postulates a relationship between increased nucleotide substitution and increased cladogenesis.

Like most aquatic plants, the pondweeds (Potamogetonaceae) are among the most phenotypically reduced and plastic of all angiosperms. As such, hypotheses of structural homology present difficulties for morphological phylogenetic reconstruction. We used non-coding nuclear and plastid DNA data to address Potamogetonaceae relationships and accompanying issues in character evolution and biogeography. Genera currently assigned to Potamogetonaceae, plus Zannichellia, formed a strongly supported monophyletic group. Potamogeton and Stuckenia (Potamogeton subg. Coleogeton) were both resolved as monophyletic. Within Potamogeton proper, two major clades followed the traditional split between broad- and narrow-leaved species, with the latter condition optimized as basal. Heterophylly (submerged plus floating leaves) has evolved several times, and the ancestral distribution for Potamogeton appears to be Northern Hemispheric. Our phylogenetic results have provided a useful genetic framework from which to interpret morphological, cytological and biogeographical evolution. ispartof: Cladistics vol:22 issue:6 pages:568-588 ispartof: location:United States status: published

A $(2+1)$-dimensional gapped quantum many-body system can have a topologically protected energy current at its edge. The magnitude of this current is determined entirely by the temperature and the chiral central charge, a quantity associated with the effective field theory of the edge. We derive a formula for the chiral central charge that, akin to the topological entanglement entropy, is completely determined by the many-body ground state wave function in the bulk. According to our formula, nonzero chiral central charge gives rise to a topological obstruction that prevents the ground state wave function from being real-valued in any local product basis., Comment: 4+6 pages, 6 figures, added references, minor changes

Species radiations have long fascinated biologists, but the contribution of adaptation to observed diversity and speciation is still an open question. Here, we explore this question using the clove genus, Syzygium, the world’s largest genus of tree species comprising approximately 1200 species. We dissect Syzygium diversity through shotgun sequencing of 182 distinct species and 58 additional as-yet unidentified taxa, and assess their genetic diversity against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that Syzygium grande shares a whole genome duplication (WGD) event with other Myrtales. Genomic analyses confirm that Syzygium originated in Sahul (Australia-New Guinea), and later diversified eastward to the Hawaiian Islands and westward in multiple independent migration events. The migrations were associated with bursts of speciation events, visible by poorly resolved branches on phylogenies and networks, some of which were likely confounded by incomplete lineage sorting. Clinal genomic variation in some sublineages follows phylogenetic progression, which coupled with sympatric occurrences of distantly related species suggests that both geographic and ecological speciation have been important in the diversification of Syzygium. Together, these results point to a mixture of both neutral and adaptive drivers having contributed to the radiation of the genus.

Quantum many-body systems involving bosonic modes or gauge fields have infinite-dimensional local Hilbert spaces which must be truncated to perform simulations of real-time dynamics on classical or quantum computers. To analyze the truncation error, we develop methods for bounding the rate of growth of local quantum numbers such as the occupation number of a mode at a lattice site, or the electric field at a lattice link. Our approach applies to various models of bosons interacting with spins or fermions, and also to both abelian and non-abelian gauge theories. We show that if states in these models are truncated by imposing an upper limit Λ on each local quantum number, and if the initial state has low local quantum numbers, then an error at most ϵ can be achieved by choosing Λ to scale polylogarithmically with ϵ−1, an exponential improvement over previous bounds based on energy conservation. For the Hubbard-Holstein model, we numerically compute a bound on Λ that achieves accuracy ϵ, obtaining significantly improved estimates in various parameter regimes. We also establish a criterion for truncating the Hamiltonian with a provable guarantee on the accuracy of time evolution. Building on that result, we formulate quantum algorithms for dynamical simulation of lattice gauge theories and of models with bosonic modes; the gate complexity depends almost linearly on spacetime volume in the former case, and almost quadratically on time in the latter case. We establish a lower bound showing that there are systems involving bosons for which this quadratic scaling with time cannot be improved. By applying our result on the truncation error in time evolution, we also prove that spectrally isolated energy eigenstates can be approximated with accuracy ϵ by truncating local quantum numbers at Λ=polylog(ϵ−1).

Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages, including angiosperms themselves. Prominently, the core eudicot lineage accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in eudicot history; however, the relative timing of these is unclear, largely due to the lack of high-quality genomes among early-diverging eudicots. Here, we provide complete genomes for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), representing the lineages most closely related to core eudicots. We show that Buxus and Tetracentron are both characterized by independent WGDs, resolve relationships among early-diverging eudicots and their respective genomes, and use the RACCROCHE pipeline to reconstruct ancestral genome structure at three key phylogenetic nodes of eudicot diversification. Our reconstructions indicate genome structure remained relatively stable during early eudicot diversification, and reject hypotheses of gamma arising via inter-lineage hybridization between ancestral eudicot lineages, involving, instead, only stem lineage core eudicot ancestors.

Continuous-variable systems protected by bosonic quantum codes have emerged as a promising platform for quantum information. To date, the design of code words has centered on optimizing the state occupation in the relevant basis to generate the distance needed for error correction. Here, we show tuning the phase degree of freedom in the design of code words can affect, and potentially enhance, the protection against Markovian errors that involve excitation exchange with the environment. As illustrations, we first consider phase engineering bosonic codes with uniform spacing in the Fock basis that correct excitation loss with a Kerr unitary and show that these modified codes feature destructive interference between error code words and, with an adapted ``two-level'' recovery, the error protection is significantly enhanced. We then study protection against energy decay with the presence of mode nonlinearities and analyze the role of phase for optimal code designs. We extend the principle of phase engineering to bosonic codes defined in other bases and multiqubit codes, demonstrating its broad applicability in quantum error correction.

New genome sequences for early-branching, aquatic flowering plants provide fresh insights into angiosperm phylogeny as well as key resources for deciphering their genome adaptive landscapes.

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in compact plant genomes. Because the small genome size of the carnivorous plant Utricularia gibba we investigate the noncoding RNA landscape and global DNA methylation in a compact genome. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of noncoding RNAs and reduced global DNA methylation levels, as determined by a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, reduced DNA methylation correlates with lack of a functional RdDM pathway, as U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs lost key domains required for complete function. Our findings unveil that lack of a functional DCL3 in U. gibba correlates with a decreased proportion of 24-nt small-interfering RNAs, low genome methylation levels, and developmental abnormalities during female gametogenesis that are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of apomixis in compact genomes.

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes. Published version The authors thank G. Alejo-Jacuinde, B. Pérez-Sánchez and Q. Ortiz-Vasquez for help collecting plants and fowering specimens. Special thanks to R. Purbojati and S. Schuster for providing us the PacBio raw sequencing data. We thank J. Cervantes-Luevano for informatic support, Luis Delaye for evolutionary analysis advice and Koribinian Schneeberger for provided us syntenic dataset generating by SyRI. Authors acknowledge Dr. T. Markow for critical review of this manuscript. S.A.C.-P., I.A.-M. and F.R.-R are the recipients of a graduate scholarship from Conacyt. Tis work was supported in part by a Senior Scholar grant from the Howard Hughes Medical Institute and a Basic Science grant from CONACytT Mexico to L.H.-E.

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.

SummaryThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation.Because the compact genome size of the carnivorous plantUtricularia gibba,we investigate in this plant the noncoding-RNA landscape and DNA methylation through a combination of cytological, evolutionary, and genome-wide transcriptomic and methylation approaches.We report an unusual distribution of noncoding RNAs inU. gibbain comparison with other characterized angiosperms, which correlated with a lower level of global genome methylation, as determined by a novel strategy based on long-read DNA sequencing and corroborated by whole-genome bisulfite analysis. Moreover, found that genes involved in the RdDM pathway may not be functionally active inU. gibba, including a truncatedDICER-LIKE 3 (DCL3),involved in the production of 24-nt small-RNAs.Our findings suggest that selective pressure to conserve a fully functional RdDM pathway might be reduced in compact genomes and a defectiveDCL3correlate with a decreased proportion of 24-nt small-RNAs and developmental alterations inU. gibba, which could represent an initial step in the evolution of apomixis.

Quantum error correction and symmetry arise in many areas of physics, including many-body systems, metrology in the presence of noise, fault-tolerant computation, and holographic quantum gravity. Here we study the compatibility of these two important principles. If a logical quantum system is encoded into $n$ physical subsystems, we say that the code is covariant with respect to a symmetry group $G$ if a $G$ transformation on the logical system can be realized by performing transformations on the individual subsystems. For a $G$-covariant code with $G$ a continuous group, we derive a lower bound on the error correction infidelity following erasure of a subsystem. This bound approaches zero when the number of subsystems $n$ or the dimension $d$ of each subsystem is large. We exhibit codes achieving approximately the same scaling of infidelity with $n$ or $d$ as the lower bound. Leveraging tools from representation theory, we prove an approximate version of the Eastin-Knill theorem: If a code admits a universal set of transversal gates and corrects erasure with fixed accuracy, then, for each logical qubit, we need a number of physical qubits per subsystem that is inversely proportional to the error parameter. We construct codes covariant with respect to the full logical unitary group, achieving good accuracy for large $d$ (using random codes) or $n$ (using codes based on $W$-states). We systematically construct codes covariant with respect to general groups, obtaining natural generalizations of qubit codes to, for instance, oscillators and rotors. In the context of the AdS/CFT correspondence, our approach provides insight into how time evolution in the bulk corresponds to time evolution on the boundary without violating the Eastin-Knill theorem, and our five-rotor code can be stacked to form a covariant holographic code., Main text 25 pages, 6 figures; see related work today by Woods and Alhambra

We construct quantum error-correcting codes that embed a finite-dimensional code space in the infinite-dimensional Hilbert state space of rotational states of a rigid body. These codes, which protect against both drift in the body's orientation and small changes in its angular momentum, may be well suited for robust storage and coherent processing of quantum information using rotational states of a polyatomic molecule. Extensions of such codes to rigid bodies with a symmetry axis are compatible with rotational states of diatomic molecules, as well as nuclear states of molecules and atoms. We also describe codes associated with general nonabelian compact Lie groups and develop orthogonality relations for coset spaces, laying the groundwork for quantum information processing with exotic configuration spaces., Comment: 28(+15) pages, 6 figures, 5 tables; v2 minor changes

Symmetry-breaking transitions are a well-understood phenomenon of closed quantum systems in quantum optics, condensed matter, and high energy physics. However, symmetry breaking in open systems is less thoroughly understood, in part due to the richer steady-state and symmetry structure that such systems possess. For the prototypical open system---a Lindbladian---a unitary symmetry can be imposed in a "weak" or a "strong" way. We characterize the possible $\mathbb{Z}_n$ symmetry breaking transitions for both cases. In the case of $\mathbb{Z}_2$, a weak-symmetry-broken phase guarantees at most a classical bit steady-state structure, while a strong-symmetry-broken phase admits a partially-protected steady-state qubit. Viewing photonic cat qubits through the lens of strong-symmetry breaking, we show how to dynamically recover the logical information after any gap-preserving strong-symmetric error; such recovery becomes perfect exponentially quickly in the number of photons. Our study forges a connection between driven-dissipative phase transitions and error correction., 5 + 6 pages

BackgroundThe genusUtriculariabelongs to Lentibulariaceae, the largest family of carnivorous plants, which includes terrestrial, epiphytic and aquatic species. The development of specialized structures that evolved for carnivory is a feature of this genus that has been of great interest to biologists since Darwin‘s early studies.Utricularia gibbais itself an aquatic plant with sophisticated bladder traps having one of the most complex suction mechanisms for trapping prey. However, the molecular characterization of the mechanisms that regulate trap development and the biophysical processes involved in prey trapping are still largely unknown due to the lack of a simple and reproducible gene transfer system.ResultsHere, we report the establishment of a simple, fast and reproducible protocol for genetic transformation ofU. gibbabased on the T-DNA ofAgrobacterium tumefaciens. An in vitro selection system using Phosphinotricin as a selective agent was established forU. gibba. Plant transformation was confirmed by histochemical GUS assays and PCR and qRT-PCR analyses. We report on the expression pattern of the 35S promoter and of the promoter of a trap-specific ribonuclease gene in transgenicU. gibbaplants.ConclusionsThe genetic transformation protocol reported here is an effective method for studying developmental biology and functional genomics of this genus of carnivorous plants and advances the utility ofU. gibbaas a model system to study developmental processes involved in trap formation.

The pseudanthial inflorescences of the sunflower family, Asteraceae, mimic a solitary flower but are composed of multiple flowers. Our studies in Gerbera hybrida indicate functional diversification for SEPALLATA (SEP)-like MADS box genes that often function redundantly in other core eudicots. We conducted phylogenetic and expression analysis for eight SEP-like GERBERA REGULATOR OF CAPITULUM DEVELOPMENT (GRCD) genes, including previously unstudied gene family members. Transgenic gerbera plants were used to infer gene functions. Adding to the previously identified stamen and carpel functions for GRCD1 and GRCD2, two partially redundant genes, GRCD4 and GRCD5, were found to be indispensable for petal development. Stepwise conversion of floral organs into leaves in the most severe RNA interference lines suggest redundant and additive GRCD activities in organ identity regulation. We show conserved and redundant functions for several GRCD genes in regulation of flower meristem maintenance, while functional diversification for three SEP1/2/4 clade genes in regulation of inflorescence meristem patterning was observed. GRCD genes show both specialized and pleiotropic functions contributing to organ differentiation and flower meristem fate, and uniquely, to patterning of the inflorescence meristem. Altogether, we provide an example of how plant reproductive evolution has used conserved genetic modules for regulating the elaborate inflorescence architecture in Asteraceae.

International audience; A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus(Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been lim-ited by low levels of sequence divergence, leading to insufficient topological resolution and statisticalsupport in phylogenetic trees, particularly for the major lineages and for the numerous species occurringin Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesisfor coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed,lab-based workflow to integrate short read next-generation sequencing for low numbers of additionalsamples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) asthe most likely ancestral locality for the origin of the coffee genus, with independent radiations acrossAfrica, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolutionof caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. Highand consistent caffeine content is found only in species from the equatorial, fully humid environmentsof West and Central Africa, possibly as an adaptive response to increased levels of pest predation.Moderate caffeine production, however, evolved at least one additional time recently (between 2 and4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already inplace during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subjectto convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate