Cette thèse s'intéresse à la conception et le développement des techniques de bioinfor- matique qui peuvent faciliter l'utilisation de l'approche metabarcoding pour mesurer la diversité d'espèces. Le metabarcoding peut être utilisé avec le séquencage haut débit pour l'identification d'espèces multiples à partir d'un seul échantillon environnemental. La véritable force du metabarcoding réside dans l'utilisation de barcode marqueurs choisi pour une étude particulière et l'identification d'espèces ou des taxons peut être réalisé avec des marqueurs soigneusement conçu. Avec l'avancement des techniques haut débit de séquençage, une énorme quantité des données de séquences est produit qui contient un nombres substantiel des mutations. Ces mutations posent un grand problème pour les estimations correctes de la biodiversité et pour le d'assignation de taxon. Les trois problèmes majeurs dans le domaine de la bioinformatique que j'ai abordés dans cette thèse sont: i) évaluer la qualité d'une barcode marker , ii) concevoir des nouveaux région barcode et iii) d'analyser les données de séquençage pour traiter les erreurs et éliminer le bruit en séquences. Pour évaluer la qualité d'un barcode marker, on a développé deux mesures quantita- tive,formelle: la couverture (Bc) et la spécificité (Bs). La couverture donne une mesure de universalité d'une pairs de primer pour amplifier un large nombre de taxa, alors que la spécificité donne une mesure de capacité à discriminer entre les différents taxons. Ces mesures sont très utiles pour le classement des barcode marker et pour sélectionner les meilleurs markers. Pour trouver des nouveaux région barcode notamment pour les applications metabarcod- ing, j'ai développé un logiciel, ecoPrimers3. Basé sur ces deux mesures de qualité et de l'information taxinomique intégré, ecoPrimers nous permet de concevoir barcode markers pour n'importe quel niveau taxonomique . En plus, avec un grand nombre de paramètres réglables il nous permet de contrôler les propriétés des amorces. Enfin, grâce a des algorithmes efficaces et programmé en langage C, ecoPrimers est suffisamment efficace pour traiter des grosses bases de données, y compris génomes bactériens entièrement séquencés. Enfin pour traiter des erreurs présentes dans les données de séquencage , nous avons analysé un ensemble simple d'échantillons de PCR obtenus à partir de l'analyse du régime alimentaire de Snow Leopard. En mesurant les corrélations entre les différents paramètres des erreurs, nous avons observé que la plupart des erreurs sont produites pendant l'amplification par PCR. Pour détecter ces erreurs, nous avons développé un algorithme utilisant les graphes, qui peuvent différencier les vrai séquences des erreurs induites par PCR. Les résultats obtenus à partir de cet algorithme a montré que les données de-bruitée a donnent une estimation réaliste de la diversité des espèces étudiées dans les Alpes françaises. / This thesis is concerned with the design and development of bioinformatics techniques that can facilitate the use of metabarcoding approach for measuring species diversity. Metabarcoding coupled with next generation sequencing techniques have a strong po- tential for multiple species identification from a single environmental sample. The real strength of metabarcoding resides in the use of barcode markers chosen for a particular study. The identification at species or higher level taxa can be achieved with carefully designed barcode markers. Moreover with the advent of high throughput sequencing techniques huge amount of sequence data is being produced that contains a substantial level of mutations. These mutations pose a problem for the correct estimates of biodi- versity and for the taxon assignation process. Thus the three major challenges that we addressed in this thesis are: evaluating the quality of a barcode region, designing new barcodes and dealing with errors occurring during different steps of an experiment. To assess the quality of a barcode region we have developed two formal quantitative mea- sures called barcode coverage (Bc) and barcode specificity (Bs). Barcode coverage is concerned with the property of a barcode to amplify a broad range of taxa, whereas barcode specificity deals with its ability to discriminate between different taxa. These measures are extremely useful especially for ranking different barcodes and selecting the best markers. To deal with the challenge of designing new barcodes for metabarcoding applications we have developed an efficient software called ecoPrimers. Based on the above two quality measures and with integrated taxonomic information, ecoPrimers1 enables us to design primers and their corresponding barcode markers for any taxonomic level. Moreover with a large number of tunable parameters it allows us to control the properties of primers. Finally, based on efficient algorithms and implemented in C language, ecoPrimers is efficient enough to deal with large data bases including fully sequenced bacterial genomes. Finally to deal with errors present in DNA sequence data, we have analyzed a simple set of PCR samples obtained from the diet analysis of snow leopard. We grouped closely related sequences and by measuring the correlation between different parameters of mutations, we have shown that most of the errors were introduced during PCR amplification. In order to deal with such errors, we have further developed an algorithm using graphs approach, that can differentiate true sequences from PCR induced errors. The results obtained from this algorithm showed that de-noised data gave a realistic estimate of species diversity studied in French Alpes. This algorithm is implemented in program obiclean.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Desde a década de 1990, os esforços internacionais para a obtenção de genomas completos levaram à determinação do genoma de inúmeros organismos. Isto, aliado ao grande avanço da computação, tem permitido o uso de abordagens inovadoras no estudo da estrutura, organização e evolução dos genomas e na predição e classificação funcional de genes. Entre os métodos mais comumente empregados nestas análises está a busca por similaridades entre sequências biológicas. Análises comparativas entre genomas completamente sequenciados indicam que cada grupo taxonômico estudado até o momento contém de 10 a 20% de genes sem homólogos reconhecíveis em outras espécies. Acredita-se que estes genes taxonomicamente restritos (TRGs) tenham um papel importante na adaptação a nichos ecológicos particulares, podendo estar envolvidos em importantes processos evolutivos. Entretanto, seu reconhecimento não é simples, sendo necessário distingui-los de ORFs não-funcionais espúrias e/ou artefatos derivados dos processos de anotação gênica. Além disso, genes espécie- ou gêneroespecíficos podem representar uma oportunidade para o desenvolvimento de métodos de identificação e/ou tipagem, tarefa relativamente complicada no caso dos procariotos, onde o método padrão-ouro na atualidade envolve a análise de um grupo de vários genes (MultiLocus Sequence Typing MLST). Neste trabalho utilizamos dados produzidos através de análises comparativas de genomas e de sequências para identificar e caracterizar genes espécie- e gênero-específicos, os quais possam auxiliar no desenvolvimento de novos métodos para identificação e/ou tipagem, além de poderem lançar luz em importantes processos evolutivos (tais como a perda e ou origem de genes em linhagens particulares, bem como a expansão de famílias de genes em linhagens específicas) nos organismos estudados. / Since the 1990s, international efforts to obtain complete genomes led to the determination of the genome of many organisms. This, coupled with great advances in computing, has allowed the use of innovative approaches in the study of structure, organization and evolution of genomes and the prediction and functional classification of genes. Among the methods most commonly employed in such analysis is the search for similarities between biological sequences. Comparative analysis of whole genome sequences indicate that each taxonomic group studied so far contain 10 to 20% of genes with no recognizable homologues in other species. It is believed that these taxonomically restricted genes (TRGs) have an important role in adaptation to particular ecological niches and may be involved in important evolutionary processes. However, the recognition of such genes is not simple, being necessary to distinguish them from spurious ORFs nonfunctional and / or artifacts from the processes of gene annotation. Furthermore, species- or genus-specific genes may be an opportunity for the development of methods for identification and / or typing, a relatively complicated task in the case of prokaryotes, where the gold standard at present involves the analysis of a group of several genes (Multilocus Sequence Typing - MLST). This study used data generated through comparative analysis of genome sequences to identify and characterize species- and genusspecific genes, which may help in the development of new methods for identification and / or typing, and can possibly shed light on important evolutionary processes (such as loss and / or origin of genes in particular lineages, as well as expansion of gene families in specific strains) involving the studied organisms.

Jahresbericht der Universitätsbibliothek Chemnitz - Berichtsjahr 2003 / Annual report of the University Library of Chemnitz in 2003

Jahresbericht der Universitätsbibliothek Chemnitz - Berichtsjahr 2004 / Annual report of the University Library of Chemnitz in 2004

Orientador: Clarisse Palma da Silva / Resumo: Áreas úmidas são ambientes na interface terrestre e aquática, onde sazonalmente a disponibilidade de água pode estar em excesso ou em escassez. A história geológica da bacia amazônica está intimamente relacionada com a presença de áreas úmidas em grandes extensões espaciais e temporais e em variadas tipologias. Dentre as tipologias de áreas úmidas presentes na Amazônia as áreas alagáveis ao longo das planícies de inundação dos grandes rios são possivelmente as que possuem maior extensão territorial. Esta tese aborda o papel das áreas úmidas para a diversidade de árvores na Amazônia. As florestas que crescem em áreas úmidas possuem menor diversidade de espécies arbóreas em relação às florestas em ambientes terrestres (i.e., florestas de terra-firme); possivelmente devido às limitações ecológicas e fisiológicas relacionadas a saturação hídrica do solo e as inundações periódicas. Entretanto, nas áreas úmidas da Amazônia já foram registradas 3,515 espécies de árvores (Capítulo 2), uma quantidade comparável à da diversidade na Floresta Atlântica. Em relação às florestas de terra-firme da Amazônia, as espécies de árvores que ocorrem em áreas úmidas tendem a apresentar maiores áreas de distribuição e amplitudes de tolerâncias de nicho ao longo da região Neotropical (Capítulo 3). A composição florística e a distância filogenética entre espécies arbóreas nas florestas de várzea da Amazônia central mudam amplamente entre localidades (Capítulo 4). O gradiente ambiental contido entre as ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Wetlands are in the interface of terrestrial and aquatic environments, where seasonally water availability may be in excess or scarcity. Geological history of Amazon basin is closely linked with a huge temporal and spatial extents of wetlands. Nowadays, floodplains (i.e., Vázea and Igapó) are the wetlands with greatest coverage in Amazon. The present thesis is focused on the role of wetlands to tree species diversity in Amazon. Wetland forests have lower tree species diversity than upland forests (i.e., Terra-Firme); most likely due to ecological and physiological limitations. Notwithstanding, in Amazonian wetland forests 3,515 tree species already were recorded, (Chapter 2), which is comparable to tree species diversity in the Atlantic Forest. Wetland tree species show greater ranges sizes and niche breadth compared to tree species do not occur in wetlands (Chapter 3). Floristic compositional turnover and phylogenetic distances between floodplain forests in Central Amazon is high (Chapter 4). The most influential driver of floristic compositional turnover was the geographic distances between localities, whereas phylogenetic distances is driven mainly by the environmental gradients between forests. Furthermore, in general, the most abundant species are those that shows greater co-occurrence associations (Chapter 5). Co-occurrence structure is influenced by biotic interactions like facilitation and competition among species, but also by niche similarities indicated in the evol... (Complete abstract click electronic access below) / Doutor

Jahresbericht der Universitätsbibliothek Chemnitz - Berichtsjahr 2003 / Annual report of the University Library of Chemnitz in 2003

Jahresbericht der Universitätsbibliothek Chemnitz - Berichtsjahr 2004 / Annual report of the University Library of Chemnitz in 2004

High-throughput Sequencing (HTS)-tekniker fortsätter att utvecklas snabbt, vilket ökar genomströmningen och minskar sannolikheten för fel. MGI Tech Co., Ltd. (MGI) är ett ledande HTS-varumärke som använder DNBSEQ-teknologi och finns i Center for Translational Microbiome (CTMR). MGI:s sequencers har en hög känslighet och det är viktigt att följa protokollen när proverna hanteras för att undvika introduktion av kontaminering. Detta projekt kommer att utforska tidigare genererade data vid CTMR för att fastställa hur och var i sekvenseringsprocessen kontaminering har introducerats. Data delas in i två huvudkategorier: primärdata, eller verkliga data (RD), och sekundära data, vidare uppdelad i Never Used Barcodes (NUB) och Non-Sequenced (NS). RD:n är sann mot provet, medan NUB och NS anses vara hämtade från bakgrundsbrus. RD, NUB och NS var föremål för taxonomiska analyser, på släkt- och artnivå, och streckkodsanalyser med hjälp av RStudio-gränssnittet för att identifiera och kontrastera de vanligaste i varje kategori. Dessutom var RD också föremål för dekontamineringsanalys på två databaser, VaMyGyn och KOLBIBAKT. Dekontaminering används för att identifiera förorenande arter i ett samhälle. Efter analysen fanns det inga starka bevis som tydde på laboratoriekontamination eller kontaminerade reagenser. Några av dessa NUB delade subsekvenser med RD barcodes, där antal reads för varje par var korrelerade mellan prover. Det kan vara en indikation på att RD barcoded med sekvenseringsfel blir inkorrekt tolkade som NUB. En djupare analys skulle krävas för att bekräfta det.CTMR är numera medveten om att kontaminering från laboratoriet, reagenser eller manipulation inte är orsaken till hämtning av bakgrundsljud. / High-throughput sequencing (HTS) technologies keep developing rapidly, increasing throughput and lowering probabilities of errors. MGI Tech Co., Ltd. (MGI) is a leading HTS brand that uses DNBSEQ technology and is present in the Centre for Translational Microbiome (CTMR). MGI’s sequencers have a high sensitivity and it is critical to follow the protocols when the samples are being handled to avoid introduction of contamination. This project will explore the previously generated data at CTMR to determine how and where in the sequencing process contamination has been introduced. Data is divided into two main categories: the primary data, or real data (RD), and secondary data, further divided into Never Used Barcodes (NUB) and Non-Sequenced (NS). The RD is true to the sample, while NUB and NS are considered background noise retrieved. The RD, NUB, and NS were subject to taxonomic analyses, at genus and species level, and barcode analyses using the RStudio interface to identify and contrast the most frequent in each category. Moreover, RD was also subject to decontam analysis on two databases, VaMyGyn and KOLBIBAKT. Decontam is used for the identification of contaminant species in a community. After the analysis, there was no strong evidence suggesting lab contamination or contaminated reagents. Some of the barcodes from NUB shared substrings with RD barcodes for which the amount of reads were correlated across samples. This may indicate that RD barcodes with sequencing errors are falsely identified as NUB, however, more analyses are needed to verify this. CTMR is now aware that contamination from the lab, reagents, or manipulation are not the causes for the background noise retrieval.