The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics [1][2][3] . These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities 4-10 . Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period 11 . Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.All grapevine varieties are highly heterozygous; preliminary data showed that there was as much as 13% sequence divergence between alleles, which would hinder reliable contig assembly when a wholegenome shotgun strategy was used for sequencing. Our consortium therefore selected the grapevine PN40024 genotype for sequencing. This line, originally derived from Pinot Noir, has been bred close to full homozygosity (estimated at about 93%) by successive selfings, permitting a high-quality whole-genome shotgun assembly.A total of 6.2 million end-reads were produced by our consortium, representing an 8.4-fold coverage of the genome. Within the assembly, performed with Arachne 12 , 316 supercontigs represent putative allelic haplotypes that constitute 11.6 million bases (Mb). These values are in good fit with the 7% residual heterozygosity of PN40024 assessed by using genetic markers. When considering only one of the haplotypes in each heterozygous region, the assembly (Table 1a) consists of 19,577 contigs (N 50 5 65.9 kilobases (kb), where N 50 corresponds to the size of the shorter supercontig or contig in a subset representing half of the assembly size) and 3,514 supercontigs (N 50 5 2.07 Mb) totalling 487 Mb. This value is close to the 475 Mb previously reported for the grapevine genome size 13 .Using a set of 409 molecular markers from the reference grapevine map 14 , 69% of the assembled 487 Mb, arranged into 45 ultracontigs

Cultivar identification is a primary concern for olive growers, breeders, and scientists. This study was aimed at examining the SSR markers retrieved from the literature and currently used in olive study, in order to select those most effective in characterizing the olive accessions and to make possible the comparison of data obtained by different laboratories. Olive microsatellite profiles were assessed by four independent laboratories, which analyzed 37 pre-selected SSR loci on a set of 21 cultivars. These SSR markers were initially tested for their reproducibility, power of discrimination and number of amplified loci/alleles. Independent segregation was tested for each pair of SSRs in a controlled cross and the allelic error rate was quantified. Some of them were finally selected as the most informative and reliable. Most of the alleles were sequenced and their sizes were determined. Profiles of the reference cultivars and a list of alleles with their sizes obtained by sequencing are reported. Several genetic parameters have been analysed on a larger set of cultivars allowing for a deeper characterization of the selected loci. Results of this study provide a list of recommended markers and protocols for olive genotyping as well as the allelic profile of a set of reference cultivars that would be useful for the establishment of a universal database of olive accessions

Ariadne is an in-progress open environment to design algorithms for computing with hybrid automata, that relies on a rigorous computable analysis theory to represent geometric objects, in order to achieve provable approximation bounds along the computations. In this paper we discuss the problem of reachability analysis of hybrid automata to decide safety properties. We describe in details the algorithm used in Ariadne to compute over-approximations of reachable sets. Then we show how it works on a simple example. Finally, we discuss the lower-approximation approach to the reachability problem and how to extend Ariadne to support it

Many natural systems exhibit a hybrid behavior characterized by a set of continuous laws which are switched by discrete events. Such behaviors can be described in a very natural way by a class of automata called hybrid automata. Their evolution are represented by both dynamical systems on dense domains and discrete transitions. Once a real system is modeled in a such framework, one may want to analyze it by applying automatic techniques, such as Model Checking or Abstract Interpretation. Unfortunately, the discrete/continuous evolutions not only provide hybrid automata of great flexibility, but they are also at the root of many undecidability phenomena. This paper addresses issues regarding the decidability of the reachability problem for hybrid automata (i.e., "can the system reach a state a from a state b?") by proposing an "inaccurate" semantics. In particular, after observing that dense sets are often abstractions of real world domains, we suggest, especially in the context of biological simulation, to avoid the ability of distinguishing between values whose distance is less than a fixed ε. On the ground of the above considerations, we propose a new semantics for first-order formulæ which guarantees the decidability of reachability. We conclude providing a paradigmatic biological example showing that the new semantics mimics the real world behavior better than the precise one

Hybrid systems are dynamical systems with the ability to describe mixed discrete-continuous evolution of a wide range of systems. Consequently, at first glance, hybrid systems appear powerful but recalcitrant, neither yielding to analysis and reasoning through a purely continuous-time modeling as with systems of differential equations, nor open to inferential processes commonly used for discrete state-transition systems such as finite state automata. A convenient and popular model, called hybrid automata, was introduced to model them and has spurred much interest on its tractability as a tool for inference and model checking in a general setting. Intuitively, a hybrid automaton is simply a "finite-state" automaton with each state augmented by continuous variables, which evolve according to a set of well-defined continuous laws, each specified separately for each state. This article investigates both the notion of hybrid automaton and the model checking problem over such a structure. In particular, it relates first-order theories and analysis results on multivalued maps and reduces the bounded reachability problem for hybrid automata whose continuous laws are expressed by inclusions (x ′ ∈ f (x, t)) to a decidability problem for first-order formulæ over the reals. Furthermore, the paper introduces a class of hybrid automata for which the reachability problem can be decided and shows that the problem of deciding whether a hybrid automaton belongs to this class can be again decided using first-order formulæ over the reals. Despite the fact that the bisimulation quotient for this class of hybrid automata can be infinite, we show that our techniques permit effective model checking for a nontrivial fragment of CTL. © 2008 Elsevier Inc. All rights reserved