La principale contribution de cette thèse est le développement d'une méthode fiable, robuste, et rapide pour la prédiction des pré-miARNs. Deux objectifs avaient été assignés : efficacité et flexibilité. L'efficacité a été rendue possible au moyen d'un algorithme quadratique. La flexibilité repose sur deux aspects, la nature des données expérimentales et la position taxonomique de l'organisme (en particulier plantes ou animaux). Mirinho accepte en entrée des séquences de génomes complets mais aussi les très nombreuses séquences résultant d'un séquençage massif de type NGS de “RNAseq”. “L'universalité” taxonomique est obtenu par la possibilité de modifier les contraintes sur les tailles de la tige (double hélice) et de la boule terminale. Dans le cas de la prédiction des miARN de plantes la plus grande longueur de leur pré-miARN conduit à des méthodes d'extraction de la structure secondaire en tige-boule moins précises. Mirinho prend en compte ce problème lui permettant de fournir des structures secondaires de pré-miARN plus semblables à celles de miRBase que les autres méthodes disponibles. Mirinho a été utilisé dans le cadre de deux questions biologiques précises l'une concernant des RNAseq l'autre de l'ADN génomique. La première question a conduit au traitement et l'analyse des données RNAseq de Acyrthosiphon pisum, le puceron du pois. L'objectif était d'identifier les miARN qui sont différentiellement exprimés au cours des quatre stades de développement de cette espèce et sont donc des candidats à la régulation des gènes au cours du développement. Pour cette analyse, nous avons développé un pipeline, appelé MirinhoPipe. La deuxieme question a permis d'aborder les problèmes liés à la prévision et l'analyse des ARN non-codants (ARNnc) dans la bactérie Mycoplasma hyopneumoniae. Alvinho a été développé pour la prédiction de cibles des miRNA autour d'une segmentation d'une séquence numérique et de la détection de la conservation des séquences entre ncRNA utilisant un graphe k-partite. Nous avons finalement abordé un problème lié à la recherche de motifs conservés dans un ensemble de séquences et pouvant ainsi correspondre à des éléments fonctionnels / The main contribution of this thesis is the development of a reliable, robust, and much faster method for the prediction of pre-miRNAs. With this method, we aimed mainly at two goals: efficiency and flexibility. Efficiency was made possible by means of a quadratic algorithm. Flexibility relies on two aspects, the input type and the organism clade. Mirinho can receive as input both a genome sequence and small RNA sequencing (sRNA-seq) data of both animal and plant species. To change from one clade to another, it suffices to change the lengths of the stem-arms and of the terminal loop. Concerning the prediction of plant miRNAs, because their pre-miRNAs are longer, the methods for extracting the hairpin secondary structure are not as accurate as for shorter sequences. With Mirinho, we also addressed this problem, which enabled to provide pre-miRNA secondary structures more similar to the ones in miRBase than the other available methods. Mirinho served as the basis to two other issues we addressed. The first issue led to the treatment and analysis of sRNA-seq data of Acyrthosiphon pisum, the pea aphid. The goal was to identify the miRNAs that are expressed during the four developmental stages of this species, allowing further biological conclusions concerning the regulatory system of such an organism. For this analysis, we developed a whole pipeline, called MirinhoPipe, at the end of which Mirinho was aggregated. We then moved on to the second issue, that involved problems related to the prediction and analysis of non-coding RNAs (ncRNAs) in the bacterium Mycoplasma hyopneumoniae. A method, called Alvinho, was thus developed for the prediction of targets in this bacterium, together with a pipeline for the segmentation of a numerical sequence and detection of conservation among ncRNA sequences using a kpartite graph. We finally addressed a problem related to motifs, that is to patterns, that may be composed of one or more parts, that appear conserved in a set of sequences and may correspond to functional elements.

Arthropod species that have the potential to damage crops are food resources for communities of predators and parasitoids. From an agronomic perspective these species are pests and biocontrol agents respectively, and the relationships between them can be important determinants of crop yield and quality. The impact of biocontrol agents on pest populations may depend on the availability of other food resources in the agroecosystem. A scarcity of such resources may limit biological control and altering agroecosystem management to alleviate this limitation could contribute to pest management. This is a tactic of ‘conservation biological control’ and includes the provision of flowers for species that consume prey as larvae but require floral resources in their adult stage. The use of flowers for pest management requires an understanding of the interactions between the flowers, pests, biocontrol agents and non-target species. Without this, attempts to enhance biological control might be ineffective or detrimental. This thesis develops our understanding in two areas which have received relatively little attention: the role of flowers in biological control by true omnivores, and the implications of flower use by fourth-trophic-level life-history omnivores. The species studied were the lacewing Micromus tasmaniae and its parasitoid Anacharis zealandica. Buckwheat flowers Fagopyrum esculentum provided floral resources and aphids Acyrthosiphon pisum served as prey. Laboratory experiments with M. tasmaniae demonstrated that although prey were required for reproduction, providing flowers increased survival and oviposition when prey abundance was low. Flowers also decreased prey consumption by the adult lacewings. These experiments therefore revealed the potential for flowers to either enhance or disrupt biological control by M. tasmaniae. Adult M. tasmaniae were collected from a crop containing a strip of flowers. Analyses to determine the presence of prey and pollen in their digestive tracts suggested that predation was more frequent than foraging in flowers. It was concluded that the flower strip probably did not affect biological control by lacewings in that field, but flowers could be significant in other situations. The lifetime fecundity of A. zealandica was greatly increased by the presence of flowers in the laboratory. Providing flowers therefore has the potential to increase parasitism of M. tasmaniae and so disrupt biological control. A. zealandica was also studied in a crop containing a flower strip. Rubidium-marking was used to investigate nectar-feeding and dispersal from the flowers. In addition, the parasitoids’ sugar compositions were determined by HPLC and used to infer feeding histories. Although further work is required to develop the use of these techniques in this system, the results suggested that A. zealandica did not exploit the flower strip. The sugar profiles suggested that honeydew had been consumed by many of the parasitoids. A simulation model was developed to explore the dynamics of aphid, lacewing and parasitoid populations with and without flowers. This suggested that if M. tasmaniae and A. zealandica responded to flowers as in the laboratory, flowers would only have a small effect on biological control within a single period of a lucerne cutting cycle. When parasitoids were present, the direct beneficial effect of flowers on the lacewing population was outweighed by increased parasitism, reducing the potential for biological control in future crops. The results presented in this thesis exemplify the complex interactions that may occur as a consequence of providing floral resources in agroecosystems and re-affirm the need for agroecology to inform the development of sustainable pest management techniques.