Finding the Core-Genes of Chloroplasts

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance

Evolution of Plant Architecture, Functional Diversification and Divergent Evolution in the Genus Atractocarpus (Rubiaceae) for New Caledonia

The diversification of ecological roles and related adaptations in closely related species within a lineage is one of the most important processes linking plant evolution and ecology. Plant architecture offers a robust framework to study these processes as it can highlight how plant structure influences plant diversification and ecological strategies. We investigated a case of gradual evolution of branching architecture in Atractocarpus spp. (Rubiaceae), forming a monophyletic group in New Caledonia that has diversified rapidly, predominantly in rainforest understory habitats. We used a transdisciplinary approach to depict architectural variations and revealed multiple evolutionary transitions from a branched (Stone's architectural model) to a monocaulous habit (Corner's architectural model), which involved the functional reduction of branches into inflorescences. We propose an integrative functional index that assesses branching incidence on functional traits influencing both assimilation and exploration functions. We showed that architectural transitions correlate with ecologically important functional traits. Variation in ecologically important traits among closely relatives, as supported by the architectural analysis, is suggestive of intense competition that favored divergence among locally coexisting species. We propose that Pleistocene climatic fluctuations causing expansion and contraction of rainforest could also have offered ecological opportunities for colonizers in addition to the process of divergent evolution

The Physics of the B Factories

This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C

Une nouvelle espèce de Thiollierea Montrouz. (Rubiaceae), micro-endémique du massif minier de Poum (Nouvelle-Calédonie)

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Status of Plectronia paradoxa Virot, myrmecophilous Rubiaceae from New Caledonia

Since the rejection of Plectronia L. versus Olinia Thunb. (Oliniaceae), some species of Rubiaceae described within this former genus have never been transferred into correct genera. The species Plectronia paradoxa Virot, endemic to New Caledonia, is a Psydra-Gaertn.' based on morphological data. A new combination is established, the description completed with the fruit characters and a drawing is provided. The presence of swollen internodes along terminal branchlets refers to a co-evolution between this plant and ants, which represents the first record of myrmecophily in the New Caledonian Rubiaceae, and the first myrmecophilous Psydrax outside Africa

On the distinction of Atractocarpus heterophyllus and A. bracteatus (Rubiaceae): in search of the correct name for the type species of Atractocarpus

International audienceAtractocarpus Schltr. & K.Krause is an Australian and Pacific genus of Gardenieae (Rubiaceae) which includes c. 40 species. The genus was initially described for a species bearing fusiform fruits, and occurring in the southern part of New Caledonia, viz. A. bracteatus Schltr. & K.Krause. Another species, A. heterophyllus (Montrouz.) Guillaumin & Beauvis. with oblong leaves and oblong ovoid fruits was described for New Caledonia, but initially under Gardenia Ellis and this for the North of the archipelago. During later revisions and supplementary descriptions of species in the genus, both species carrying heteromorphic leaves were reconsidered. The name A. bracteatus was placed in synonymy of A. heterophyllus; while keeping a delimitation of the species restricted to the southeastern populations. This situation ended in the re-description of the northern species, named A. balansaeanus Guillaumin. The results of the present work, based on the examination of herbarium specimens and literature, disentangles the collusion for A. heterophyllus vs A. bracteatus. Hence, the correct name typifying Atractocarpus is A. bracteatus. In regard to the destruction of the holotype for A. bracteatus in Berlin (B) and of two of the syntypes for A. heterophyllus in Lyon (LYJB), typifications for these species names are proposed. To clarify their taxonomy, complete descriptions, lists of specimens and illustrations are provided for both species

Statut de Plectronia paradoxa Virot, Rubiaceae myrmécophile de Nouvelle-Calédonie

International audienceDepuis le rejet du genre Plectronia L. contre Olinia Th unb. (Oliniaceae), certaines Rubiaceae décrites à tort sous ce genre n'ont toujours pas été transférées dans les genres adéquats. Ainsi l'espèce Plectronia paradoxa Virot, endémique de Nouvelle-Calédonie, est attribuée ici au genre Psydrax Gaertn., sur la base de données morphologiques. Une nouvelle combinaison est établie, la description de l'espèce est complétée par les caractères des fruits et une illustration est fournie. La présence d'entrenoeuds renfl és marque une tendance à la co-évolution de la plante avec les fourmis, constituant la première mention de myrmécophilie chez les Rubiaceae de cet archipel du Pacifi que et le premier Psydrax myrmécophile non africain

Les Rubiaceae émergentes de la canopée endémiques de l'archipel des Comores : affinités floristiques dans l'océan Indien et taxonomie

International audienceL'archipel des Comores est riche en espèces de la famille des Rubiaceae, mais cette famille comprend seulement trois arbres émergeant de la canopée forestière humide. La première espèce, Gyrostipula comorensis Homolle ex J.-F.Leroy, de la tribu des Naucleeae, connue à la Grande Comore et à Mohéli voit sa distribution élargie à Anjouan, devenant une espèce endémique de l'Union des Comores dans sa totalité. Une description amendée est proposée, d'après des récoltes récentes. Les deux autres espèces, de la tribu des Vanguerieae, sont endémiques de Mayotte et placées dans les genres Peponidium et Pyrostria. Peponidium ovatooblongum (K.Schum.) Mouly, nouvellement combiné ici, avait préalablement été placé sous Psychotria avec doute, alors qu'un nom postérieur, Peponidium comorense placé ici en synonymie, a également été publié. Pyrostria heliconioides Mouly, nouvellement décrit, porte des inflorescences spathiformes tout à fait remarquables dans le genre. Ces trois espèces restreintes à l'archipel possèdent ostensiblement des affinités avec les Rubiaceae malgaches

Validation of the name Cyclophyllum memaoyaense, a rare species in New Caledonia

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