No description available.

Les volumes des données générées par les technologies de séquençage haut débit augmentent exponentiellement ce dernier temps. Le stockage, le traitement et le transfertdeviennent des défis de plus en plus sérieux. Pour les affronter, les scientifiques doivent élaborer des approches et des algorithmes de plus en plus efficaces.Dans cette thèse, nous présentons des structures de données efficaces etdes algorithmes pour des problèmes de recherche approchée de chaînes de caractères, d'assemblagedu génome, de compression de séquences d’ADN et de classificationmétagénomique de lectures d’ADN.Le problème de recherche approchée a été bien étudié, avec un grandnombre de travaux publiés. Dans ledomaine de bioinformatique, le problème d’alignement de séquences peut être considéré comme unproblème de recherche approchée de chaînes de caractères. Dans notre travail, nousétudions une stratégie de recherche basée sur une structure d'indexation ditebidirectionnelle. D’abord, nous définissons un formalisme des schémas de recherche pour travailleravec les stratégies de recherche de ce type, ensuite nous fixons une mesure probabiliste del’efficacité de schémas de recherche et démontrons quelques propriétés combinatoires de schémasde recherche efficaces. Finalement, nous présentons des calculs expérimentaux quivalident la supériorité de nos stratégies. L’assemblage du génome est un des problèmes clefs en bioinformatique.Dans cette thèse, nous présentons une structure de données — filtre de Bloom en Cascade— qui améliore le filtre de Bloom standard et peut être utilisé pour larésolution de certains problèmes, y compris pour l’assemblage du génome. Nousdémontrons ensuite des résultats analytiques et expérimentaux sur les propriétés du filtre deBloom en Cascade. Nous présentons également comment le filtre de Bloom en Cascade peut être appliqué au problèmede compression de séquences d’ADN.Un autre problème que nous étudions dans cette thèse est la classificationmétagénomique de lectures d’ADN. Nous présentons une approche basée sur la transforméede Burrows-Wheeler pour la recherche efficace et rapide de k-mers (mots de longueur k).Cette étude est centrée sur les structures des données qui améliorent lavitesse et la consommation de mémoire par rapport à l'index classique de Burrows-Wheeler, dans le cadre de notre application / Amounts of data generated by Next Generation Sequencing technologies increase exponentially in recent years. Storing, processing and transferring this data become more and more challenging tasks. To be able to cope with them, data scientists should develop more and more efficient approaches and techniques.In this thesis we present efficient data structures and algorithmic methods for the problems of approximate string matching, genome assembly, read compression and taxonomy based metagenomic classification.Approximate string matching is an extensively studied problem with countless number of published papers, both theoretical and practical. In bioinformatics, read mapping problem can be regarded as approximate string matching. Here we study string matching strategies based on bidirectional indices. We define a framework, called search schemes, to work with search strategies of this type, then provide a probabilistic measure for the efficiency of search schemes, prove several combinatorial properties of efficient search schemes and provide experimental computations supporting the superiority of our strategies.Genome assembly is one of the basic problems of bioinformatics. Here we present Cascading Bloom filter data structure, that improves standard Bloom filter and can be applied to several problems like genome assembly. We provide theoretical and experimental results proving properties of Cascading Bloom filter. We also show how Cascading Bloom filter can be used for solving another important problem of read compression.Another problem studied in this thesis is metagenomic classification. We present a BWT-based approach that improves the BWT-index for quick and memory-efficient k-mer search. We mainly focus on data structures that improve speed and memory usage of classical BWT-index for our application

Aim Morinda citrifolia L., commercially known as noni or the Indian mulberry plant, is morphologically variable and the only widely distributed member of the pantropical genus Morinda sensu stricto (Rubiaceae). This large distribution has been attributed partly to the ability of the seeds of the large-fruited M. citrifolia L. var. citrifolia L. to be transported by oceanic drifting. This form of M. citrifolia var. citrifolia has been predicted to be the progenitor colonizer of the island endemic Morinda species. Using a phylogenetic approach and large sampling of the widespread, large-fruited M. citrifolia var. citrifolia, we assessed the potential area of origin of M. citrifolia and tested the hypothesis that the large-fruited M. citrifolia var. citrifolia is an ancestral colonizer. Location Tropics. Methods We performed Bayesian analyses of 22 species of the tribe Morindeae (including 11 individuals of the three currently recognized varieties of M. citrifolia) based on combined nrETS, nrITS, rps16 and trnT-F sequence data. Geographic origins of the studied taxa were mapped onto the Bayesian majority rule consensus tree. Results Nine sequenced individuals of M. citrifolia from diverse geographic locations formed a highly supported clade, which was sister to the Australo-Micronesian clade that included M. bracteata var. celebica and M. latibracteata. These sister clades are part of the broader Asian, arborescent Morinda clade. We found no support for the current varietal classification of M. citrifolia. Main conclusions Our analyses suggest a Micronesian origin of M. citrifolia. This implies that the large-fruited M. citrifolia var. citrifolia might well have been present in the Pacific before the arrival of the Micronesian and Polynesian ancestors from Southeast Asia. The wide distribution of this form of M. citrifolia var. citrifolia is attributed partly to the trans-oceanic dispersal of its buoyant seeds, self-pollination and its ability to produce flowers and fruits year-round. The hypothesis that the widespread, large-fruited M. citrifolia var. citrifolia is the progenitor colonizer of the island endemic Morinda species is inconsistent with its derived position within the Asian, arborescent Morinda clade and with the fact that the nine sampled individuals of M. citrifolia form a clade.

<p>This thesis deals with evolutionary relationships within the asterids, a group of plants comprising about one-third of all flowering plants.</p><p>Two new families are recognised: Pennantiaceae and Stemonuraceae. The woody <i>Pennantia</i> from New Zealand and Australia is the sole genus of Pennantiaceae. Stemonuraceae consist of a dozen woody genera with a pantropical distribution and a centre of diversity in South East Asia and the Malesian islands. They are characterised by long hairs on their stamens and/or fleshy appendages on their fruits. Both families were formerly included in Icacinaceae. While Pennantiaceae are unrelated to any of the former Icacinaceae and placed in the order Apiales, other former Icacinaceae genera are related to <i>Cardiopteris</i>, a twining herb from South East Asia and Malesia. The monogeneric family Cardiopteridaceae is enlarged as to include also these. Cardiopteridaceae and Stemonuraceae are sister groups and placed in Aquifoliales. The three other families of Aquifoliales are monogeneric and closely related. The Asian Helwingiaceae and the Central/South American Phyllonomaceae are suggested to be merged into Aquifoliaceae (hollies). The genera of Icacinaceae in the traditional sense not placed in any of the above families (all euasterids II) are members of early diverging lineages of the euasterids I and possibly included in the order Garryales.</p><p>The three woody Australasian families Alseuosmiaceae, Argophyllaceae, and Phellinaceae are confirmed as members of Asterales, despite traditional placements not close to that order. They are, moreover, supported as each other’s closest relatives.</p><p>The results are based mainly on parsimony analysis of DNA sequence data, but morphological studies have revealed characters in support for the molecularly based conclusions. The gene that has provided most new information is the chloroplast <i>ndh</i>F gene. The results are, however, drawn from combined analyses of sequences from one or several additional genes (<i>atp</i>B, <i>mat</i>K, <i>rbc</i>L, <i>18S</i> rDNA). The data have also been explored with Bayesian analysis, a statistical, model-based method that most recently has been developed for phylogeny reconstruction.</p>

This thesis deals with evolutionary relationships within the asterids, a group of plants comprising about one-third of all flowering plants. Two new families are recognised: Pennantiaceae and Stemonuraceae. The woody Pennantia from New Zealand and Australia is the sole genus of Pennantiaceae. Stemonuraceae consist of a dozen woody genera with a pantropical distribution and a centre of diversity in South East Asia and the Malesian islands. They are characterised by long hairs on their stamens and/or fleshy appendages on their fruits. Both families were formerly included in Icacinaceae. While Pennantiaceae are unrelated to any of the former Icacinaceae and placed in the order Apiales, other former Icacinaceae genera are related to Cardiopteris, a twining herb from South East Asia and Malesia. The monogeneric family Cardiopteridaceae is enlarged as to include also these. Cardiopteridaceae and Stemonuraceae are sister groups and placed in Aquifoliales. The three other families of Aquifoliales are monogeneric and closely related. The Asian Helwingiaceae and the Central/South American Phyllonomaceae are suggested to be merged into Aquifoliaceae (hollies). The genera of Icacinaceae in the traditional sense not placed in any of the above families (all euasterids II) are members of early diverging lineages of the euasterids I and possibly included in the order Garryales. The three woody Australasian families Alseuosmiaceae, Argophyllaceae, and Phellinaceae are confirmed as members of Asterales, despite traditional placements not close to that order. They are, moreover, supported as each other’s closest relatives. The results are based mainly on parsimony analysis of DNA sequence data, but morphological studies have revealed characters in support for the molecularly based conclusions. The gene that has provided most new information is the chloroplast ndhF gene. The results are, however, drawn from combined analyses of sequences from one or several additional genes (atpB, matK, rbcL, 18S rDNA). The data have also been explored with Bayesian analysis, a statistical, model-based method that most recently has been developed for phylogeny reconstruction.

MSCAGR (Plant Production) / Department of Plant Production / See the attached abstract below