Master of Science / Department of Computing and Information Sciences / Doina Caragea / This study is a comparison and exploration of next generation sequencing algorithms and tools. A simulation study was done to compare the performance of edgeR, DESeq, and baySeq in detecting differential gene expression. The methods were compared in context of a balanced pairwise design. The simulation results suggest that the methods are compa- rable under the conditions simulated. The study also explored real data comprised of one biological replicate between two treatments. Cufflinks and CummerRBund were used to detect differential gene expression. The visualization results from the real data suggest no differential expression is present.

The rapid and reliable detection of pathogens is of utmost importance in healthcare settings to ensure the appropriate treatment thereby reducing morbidity and mortality for the patient. Current culturing, PCR based and NGS species detection methods are time consuming (Opota et al., 2015), limited in their detection (Buckley et al., 2015), or require specialist skills and are expensive (Basho and Eterovic., 2015). Oxford Technologies Nanopore devices could provide detailed genomic sequencing at a fraction of the cost and without the need for technical bioinformatic skills. This study evaluates the MinION device and analysis tools to suggest best practice. Classification and genotyping of 12 Klebsiella isolates were performed using EPI2ME automated workflows and manual de novo assembly.  Automated workflows using raw MinION reads provided clinically relevant information identified in ~6hrs. Manual de novo assembly and analysis used hybrid, and single source data took >24hrs. The inclusion of MinION long reads overcome problems assembling short reads. Hybrid genomes provided the most contiguous and highly detailed contigs. MinION only read assemblies contained more errors but still identified similar genotypic findings. Automated workflows are rapid and require minimal bioinformatic know-how. There should be a dialogue between clinicians and bioinformaticians to develop bespoke analysis tools.  Although challenges remain around compatible kits and vulnerable flowcells long read sequencing can be an effective tool for species detection and pathogen typing. Furthermore, hybrid assemblies have the potential to advance our genome detailing and discovery.

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2018-04-16T17:42:56Z No. of bitstreams: 2 Dissertação - Andrezza Arantes Castro - 2018.pdf: 2625041 bytes, checksum: 5c588cc8e4644fe3bfa34ba8e1dd05a9 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-04-17T10:54:33Z (GMT) No. of bitstreams: 2 Dissertação - Andrezza Arantes Castro - 2018.pdf: 2625041 bytes, checksum: 5c588cc8e4644fe3bfa34ba8e1dd05a9 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-17T10:54:33Z (GMT). No. of bitstreams: 2 Dissertação - Andrezza Arantes Castro - 2018.pdf: 2625041 bytes, checksum: 5c588cc8e4644fe3bfa34ba8e1dd05a9 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-03-12 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / The ease access to Next Generation Sequence methodologies has improved the development of several projects, once it makes possible the de novo assembly of DNA sequences, creating a great amount of data and giving access to unknown genomes of different organisms. The anuran species Ololygon centralis belong to Hylidae family. It is considered as endemic of Cerrado Biome and little is known about its genomics. The aim of this work was to realize a draft of the genome of O. centralis in order to identify, to characterize, to quantify repetitive elements and to predict possible genes. Also, we aimed to develop microsatellite markers for the species. The genome draft assembled in 13989 scaffolds, which correspond to 4926069 bp with N50 = 336. The repetitive elements found in the O. centralis genome (1795 transposons, 957, microsatellite, one satellite DNA and 25 small nuclear RNAs) comprised 531337 bp. Between the retrotransposons, the LINE element (49,83%) was the most abundant, followed by LTR (48,66%) and SINE (1,56%). It was possible to identify coding genes for the 5S, 18S and 28S subunits of ribosomes. Also, 18 types of coding regions for tRNA and 26 putative genes were found in the O. centralis genome. From the microsatellite regions, it was possible to design 87 pairs of primers for the flanking sites. There were found 47 regions composed of tetranucleotides, 39 dinucleotides and on trinucleotide on the microsatellite sites. From them, 31 pairs of primers were selected for amplification and 18 showed good results. The annealing temperatures varied from 50° e 60° C. Seven markers showed polymorphism. From them, only 5 markers (PCE05, OCE11, PCE20, OCE21, OCE26) were used to characterize the genotype of 30 individuals. The medium number of alleles was 10, the allelic amplitude varied from 148 bp (OCE20) to 318 bp (OCE21). The Expected Heterozygosity was 0,7 and the observed was 0,5. The probability of parentage exclusion (Q) was 0,993 and the probability of combined identity (I) was 1,13x10-6. The global value of the fixation index (FST) was significant and equal to 0,2 (p<0.05). The data obtained from the NGS Illumina platform represent one important step for the knowledge of genomics of this species and of the anuran in general. / A facilidade para o acesso às metodologias de Sequenciamento de Segunda Geração (Next Generation Sequence) tem impulsionado o desenvolvimento de diversos projetos, uma vez que possibilita a montagem de novo de sequências, gerando uma grande quantidade de dados e permitindo o acesso a genomas de diversos organismos ainda pouco conhecidos. A espécie de anuro Ololygon centralis (Pombal e Bastos 1996) pertence à família Hylidae, considerada endêmica do Bioma Cerrado e que ainda não dispõe de nenhuma informação genômica. O objetivo desse trabalho foi realizar uma montagem parcial do genoma de Ololygon centralis a fim de identificar, caracterizar, quantificar elementos repetitivos e predizer genes nas sequências genômicas, além de desenvolver marcadores microssatélites para a espécie. O genoma parcial montado resultou em 13.989 scaffolds, que correspondem a 4.926.069 pb com N50 de 336. Os elementos repetitivos encontrados no genoma de O. centralis (1.795 elementos transponíveis, 957 microssatélites, um DNA satélite e 25 pequenos RNAs nucleares) totalizaram 531.337 pb. Entre os retrotransposons, o elemento LINE (49,83%) foi o mais abundante, seguido do LTR (48,66%) e SINE (1,56%). Foram identificados os genes que codificam as subunidades 5S, 18S e 28S de ribossomos, 18 tipos de tRNAs no genoma e 26 genes. A partir das sequências foi possível desenhar 87 pares de primers flanqueando regiões microssatélites. Dentre elas, 47 foram regiões compostas de tetranucleotídeos, 39 dinucleotídeos, e um trinucleotídeo. Deste total, 31 pares de primers foram selecionados para padronização em gel de poliacrilamida (6%) e 18 deles apresentaram produto de amplificação adequado. Durante a padronização, as temperaturas de anelamento variaram entre 50° e 60° C e sete marcadores apresentaram polimorfismo. Dos sete, apenas cinco marcadores (OCE05, OCE11, OCE20, OCE21, OCE26) foram padronizados e utilizados para caracterização em 30 indivíduos de O. centralis no analisador automático ABI3500. O número médio de alelos foi igual a 10, a amplitude alélica variou entre 148pb (OCE 20) a 318 pb (OCE 21). A Heterozigosidade média esperada foi 0,7 e a observada igual a 0,5. A probabilidade de exclusão de paternidade (Q) foi igual a 0,993 e a probabilidade combinada de identidade (I) igual a 1,13x10-6. O valor global para o índice de fixação (FST) foi significativo e igual a 0,2 (p <0,05). Os dados obtidos a partir do NGS plataforma Illumina representam um importante passo para o conhecimento genômico dessa espécie e dos anfíbios em geral, o desenvolvimento de primers contribuirá para o estudos genéticos-populacionais de Ololygon centralis e espécies correlacionadas por meio da transferibilidade.

Atlantic salmon is a species of both scientific and economic importance, and Atlantic salmon farming is a highly profitable industry worldwide. One of the biggest challenges being faced by farms, which affects production efficiency and results in severe economic loss, is disease. In livestock production, one of the approaches taken to limit the impact of disease outbreaks is to selectively breed for improved resistance within farmed populations. Although traditional family-based resistance breeding programs have shown improvements in resistance to a variety of bacterial, viral and parasitic diseases on Atlantic salmon farms, response to selection can be slow. One way of increasing selection efficiency is through the incorporation of genetic markers into breeding programs, for marker-assisted or genomic selection. However, genomic resources for cultured aquatic species are sparse, and the generation of new and denser resources for use in selective breeding programs would be advantageous. The main focus of this thesis is the development of genomic resources in Atlantic salmon and the application of those resources to gain a better understanding of the salmon genome, particularly in the genetic basis of host resistance to infectious diseases. The first aim of this thesis was to develop improved genomic resources for Atlantic salmon, and to characterise the Atlantic salmon genome via construction and analysis of a SNP linkage map derived from RAD-Sequencing (RAD-Seq). Approximately 6,500 SNPs were assigned to 29 linkage groups, and ~1,800 male-segregating, and ~1,400 female-segregating SNPs were ordered and positioned. Overall map lengths and recombination ratios were relatively consistent between the sexes and across the linkage groups (~1:1.5, male:female). However, a substantial difference in the degree of marker clustering was seen between males and females, which is reflective of the difference in the positions of chiasmata between the two sexes. Using this map, ~4,000 Atlantic salmon reference genome contigs were assigned to a linkage group, and 112 contigs were assigned to multiple linkage groups, highlighting regions of homeology (large sections of duplicated chromosomal regions) within the salmon genome. Alignment of SNP-flanking sequences to the stickleback and rainbow trout genomes identified putative gene-associated SNPs and cross-species chromosomal orthologies, and provided evidence in support of the salmonid-specific genome duplication. In addition, based on this and other publically available RAD-Seq datasets, the utility of RAD-Seq-derived data from different species and laboratories for population genetics analyses was tested. Short RAD-Seq contigs in Atlantic salmon and nine other teleost fish were used to identify cross-species orthologous genomic relationships. Several thousands of orthologous RAD loci were identified across the species, with the number of RAD loci decreasing with evolutionary distance, as expected. Previously published broad-level relationships between orthologous chromosomes were confirmed. The identified cross-species orthologous RAD loci were used to estimate evolutionary relationships between the ten teleost fish species. Previously published relationships were recovered, suggesting that RAD-Seq data derived from different laboratories is useful for this purpose. The second aim was to characterise the genetic architecture of resistance to two viral diseases affecting Atlantic salmon production on farms: pancreas disease (PD), and infectious pancreatic necrosis (IPN). Using data and samples collected from a large population of salmon fry challenged with PD, a high heritability for resistance was estimated (h2 ~0.5), and four QTL were identified, on chromosomes 3, 4, 7 and 23. The QTL explaining the highest within-family variation for resistance was located on chromosome 3. This QTL has been confirmed in a population of post-smolts by an independent research group, highlighting the potential for its incorporation into breeding programs to improve PD resistance. For IPN, the major resistance QTL had previously been mapped to linkage group 21. However, the mutation(s) underlying this QTL effect and the consequences of these mutation(s) on the affected genes and relevant biological resistance mechanisms are unknown. To generate a list of candidate genes within the vicinity of the IPN QTL, QTL-linked DNA sequences were aligned to four model fish genomes. This identified two QTL-orthologous regions in each of the species, and gene order within these regions was highly conserved across species. Analysis of gene expression patterns between IPN resistant and susceptible salmon in a viral challenge experiment revealed that the five most significantly differentially-expressed genes mapped to the QTL-orthologous region on linkage group II of stickleback. Pathway enrichment analysis across all differentially-expressed genes suggests that biological pathways influencing viral infection stress response/entry/replication, cellular energy production and apoptosis may be involved in resistance during the initial stages of IPN virus (IPNV) infection. These results have provided the basis for further study of the putative involvement of these candidate genes and pathways in genetic resistance to IPNV. In summary, the results and resources presented in this thesis extend our current understanding of the salmon genome and the genetic basis of resistance to two viral diseases, and provide resources with the potential to be used in Atlantic salmon selective breeding programs to tackle disease outbreaks.

Modern agriculture is dependent on both global supply chains and crop monocultures. These features aid the evolution and spread of novel plant pathogens. Limited genetic diversity in commercial crop lines can result in widespread susceptibility to emerging pathogens. Pathogen resistance may be developed through conventional breeding approaches, or a number of transgenic strategies. This thesis focuses on the characterisation of an emerging maize disease, Maize lethal necrosis (MLN), and engineering resistant maize lines using an artificial microRNA (amiRNA) approach. MLN is a synergistic viral disease caused by the interaction of Maize chlorotic mottle virus (MCMV) with any maize-infecting member of the potyviridae. I used next-generation RNA sequencing to characterise the MLN outbreak in East Africa, discovering that local and Chinese strains of the potyvirus Sugarcane mosaic virus (SCMV) typically coinfect with MCMV. A first global MCMV phylogeny was constructed using these samples combined with new Sanger sequencing of samples in Ecuador and Hawaii. The phylogeny supported previous hypotheses of a link between the Chinese and African outbreaks, and suggested a novel link between the Hawaiian and Ecuadorian outbreaks. The SCMV sequences generated demonstrated strong evidence of extensive recombination, in line with previous reports on SCMV and potyviruses. These data also produced first reports of a number of RNA viruses in East Africa, and five novel viral-like sequences, with their presence confirmed by RT-PCR. RNA silencing is an important component of the plant immune response to viral infection. amiRNAs can be used to generate specific and effective viral resistance through Watson- Crick base pairing between the amiRNA and the (RNA) viral genome. Previous amiRNA approaches have targeted invariable genomic regions using consensus sequences. However, the high mutation rate of RNA viruses means single cells contain a variety of mutant genomes, collectively called a quasispecies. To deter the evolution of resistance breaking I devised a novel strategy to include intra-sample variation from NGS data in amiRNA design, and constructs, each containing five of these amiRNAs, were transformed into tropical maize lines. RNA silencing may be hampered by the expression of viral suppressors of silencing (VSRs). Local VSR assays demonstrated that there are no local VSRs in the MCMV genome, while systemic VSR assays showed a possible systemic VSR role for the unique P32 protein, and an interesting link between photoperiod and systemic silencing more generally.

Biodiversity across the globe is threatened. Rapid surveying and monitoring techniques are required to understand the origin of the threats to biodiversity and to enable conservation actions to be undertaken. Kuwait is an arid desert country with a small flora of only 402 species. This flora is endangered by environmental factors, overgrazing, and human activities. DNA barcoding the flora and using Next Generation Sequencing (NGS) technologies allowed us to identify plants to species level, conduct a molecular taxonomic revision, and distinguish plant diversity found in soil environmental DNA samples. After investigating the discriminatory power of five commonly used DNA markers from plastid (matK, rbcL, trnH-psbA, trnL) and a nuclear genome (ITS2) on four largest genera of the flora using phylogenetics reconstruction tree based methods, two barcoding markers (rbcL and ITS2) were assigned to build a DNA reference library of the flora. Furthermore, the DNA reference library was tested to identify the plant diversity found below-ground level and comparing it with that above-ground, using environmental soil samples collected from both species rich and poor habitats in Kuwait by applying high-throughput sequencing methods. The DNA database provided in this study could be used as a reference library for the identification process and contribute towards the future of molecular taxonomy, biodiversity and ecological research in Kuwait.

Submitted by Paulo Henrique Jorge (paulohj@ibb.unesp.br) on 2016-09-21T21:22:43Z No. of bitstreams: 1 Tese Paulo.pdf: 2340897 bytes, checksum: 4d1a3bab6d4520ebb58d8720feafa105 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-09-22T18:14:15Z (GMT) No. of bitstreams: 1 jorge_ph_me_bot.pdf: 2340897 bytes, checksum: 4d1a3bab6d4520ebb58d8720feafa105 (MD5) / Made available in DSpace on 2016-09-22T18:14:15Z (GMT). No. of bitstreams: 1 jorge_ph_me_bot.pdf: 2340897 bytes, checksum: 4d1a3bab6d4520ebb58d8720feafa105 (MD5) Previous issue date: 2016-02-25 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / A pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), é um peixe de ocorrência na bacia Amazônica e uma das principais espécies nativas utilizadas para a produção em aquicultura. O principal objetivo deste estudo foi realizar o sequenciamento do transcriptoma de P. brachypomus por meio de Sequenciamento de Nova Geração (NGS) e, em seguida, caracterizar um conjunto de marcadores microssatélites para esta espécie. Além disso, marcadores microssatélites polimórficos foram usados para realizar a análise da variabilidade genética em estoques cultivados de pirapitinga. O sequenciamento do transcriptoma foi realizado por meio da tecnologia 454/Roche, que resultou em 3.696 contigs não reduntantes (nr). Destes 2.568 genes com correspondência no banco de proteínas (nr) foram caracterizados nas categorias de Gene Ontology (GO), sendo que 2.075 sequências (80,8%) foram anotadas em termos GO. Dos 30 loci de microssatélites, após o processo validação, 8 loci de microssatélites demonstraram polimorfismo. A análise desses marcadores polimórficos em estoques cultivados revelou que as pisciculturas do Norte apresentaram uma maior variabilidade genética (riqueza de alelos e heterozigosidade) do que as Pisciculturas do Sudeste. Além disso, os resultados da AMOVA demonstraram que a maior variação estava presente dentro das populações (62,5%). Entretanto, quando comparado os grupos de acordo com a origem (Selvagem, Pisciculturas do Norte e Pisciculturas do Sudeste), foi verificada uma variação considerável (31,76%) entre os grupos. Estes dados foram corroborados com os valores de Fst, pois houve alta estruturação genética entre os estoques cultivados e a população selvagem, bem como também entre as Pisciculturas do Norte e do Sudeste. A estratégia de sequenciamento do transcriptoma por NGS se demonstrou eficaz na prospecção de marcadores moleculares, além de gerar um alto volume de recursos genéticos para serem explorados em diversas áreas da biologia. Os microssatélites gerados nesse estudo são importantes ferramentas para serem empregadas no manejo genético de estoques de reprodutores cultivados, o que poderá aumentar a produtividade em sistemas de produção e gerar um alto valor agregado do pescado com qualidade genética. / The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish that occurrs in the Amazon basin and it is considered as one of the main native species used for production in aquaculture in South America. The main objectives of this study were: 1) to perform the transcriptome sequencing of P. brachypomus through Next Generation Sequencing (NGS) and then characterize a set of microsatellite markers for this species; 2) to apply microsatellite polymorphic markers for analysis of genetic variability in cultured stocks of pirapitinga. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant (nr) contigs. Of these total, 2,568 genes had similarity in the protein database nr (Genbank) and were characterized in the categories of Gene Ontology (GO), with 2,075 sequences (80.8%) annotated in GO terms. After the validation process of 30 microsatellite loci, 8 microsatellite markers showed polymorphism. The analysis of these polymorphic markers in cultured stocks revealed that the Northern fish farms had a higher genetic diversity (allele richness and heterozygosity) than the Southeastern fish farms. In addition, the AMOVA results demonstrated the highest variation present within the populations (62.5%). However, when comparing the groups according to the geographic distribution (Wild, North Fish farms and fish farms in the Southeast), it was observed a considerable variation (31.76%) among the groups. The Fst values showed there is a genetic structure among the broodstocks analyzed. Microsatellites generated by transcriptome sequencing in this study are important tools to be used in the genetic management of cultivated breeding stocks, as well to identify different gene banks, which might provide a basis for a genetic pre-breeding program in pirapitinga. / FAPESP: 2014/05732-2

Made available in DSpace on 2016-09-27T13:40:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-11-04. Added 1 bitstream(s) on 2016-09-27T13:45:09Z : No. of bitstreams: 1 000870647.pdf: 1368263 bytes, checksum: dbbed6b733deb8dc0c8f5c1073fd25c8 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Taenia saginata representa uma ameaça à segurança alimentar e à saúde pública devido à infecção pela ingestão de carne mal cozida e contaminada. Esta zoonose está amplamente distribuída, afetando humanos, os hospedeiros definitivos, e bovinos, hospedeiros intermediários. Além disto, a cisticercose bovina é responsável por perdas econômicas significativas devido à condenação de carcaças infectadas. A estratégia fundamental para o controle do complexo teníase-cisticercose consiste em interromper o ciclo evolutivo do parasita, evitando assim a infecção nos animais e no homem. Assim, a principal medida praticada no Brasil tem sido a inspeção de carcaças durante o abate, a qual é também a forma mais comum de diagnóstico. A insuficiente informação molecular de T. saginata tem dificultado o avanço das pesquisas para o aprimoramento de testes diagnósticos, o desenvolvimento de vacinas e a identificação de novas drogas para tratamento. Com o intuito de adquirir informação sobre o estágio de desenvolvimento metacestóide do parasita, foi utilizada a tecnologia de RNAseq para a montagem do transcriptoma de metacestóide de T. saginata. Estes dados serão úteis para estudos futuros envolvendo triagem para diagnóstico e marcadores imunoprofiláticos para a cisticercose bovina / Taenia saginata represents a threat to food security and public health in consequence of human infection by ingestion of contaminated undercooked meat. This zoonosis is worldwide distributed, affecting human, definitive host, and bovine, intermediate host. Besides, bovine cysticercosis is responsible for significant economic losses due to the condemnation of infected carcasses. The main strategy to control taeniasis-cysticercosis complex consists of interrupting the parasite's biological cycle, thus preventing human and animal infection. Therefore, in Brasil the main control measure has been the carcass inspection during the slaughter, which is also the most common diagnostic practice. Insufficient T. saginata molecular information makes difficult consistent advances to the improvement of diagnostic tests, vaccine development and the identification of new drugs for treatment. In order to gain insights about the parasite's metacestode developmental stage, RNAseq technology was used to assemble the whole transcriptome of a T. saginata metacestode. These data will also be useful for the next generation screening studies of diagnostic and immunoprophylatic markers for bovine cysticercosis

Orientador: Diogo Teruo Hashimoto / Resumo: The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish that occurrs in the Amazon basin and it is considered as one of the main native species used for production in aquaculture in South America. The main objectives of this study were: 1) to perform the transcriptome sequencing of P. brachypomus through Next Generation Sequencing (NGS) and then characterize a set of microsatellite markers for this species; 2) to apply microsatellite polymorphic markers for analysis of genetic variability in cultured stocks of pirapitinga. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant (nr) contigs. Of these total, 2,568 genes had similarity in the protein database nr (Genbank) and were characterized in the categories of Gene Ontology (GO), with 2,075 sequences (80.8%) annotated in GO terms. After the validation process of 30 microsatellite loci, 8 microsatellite markers showed polymorphism. The analysis of these polymorphic markers in cultured stocks revealed that the Northern fish farms had a higher genetic diversity (allele richness and heterozygosity) than the Southeastern fish farms. In addition, the AMOVA results demonstrated the highest variation present within the populations (62.5%). However, when comparing the groups according to the geographic distribution (Wild, North Fish farms and fish farms in the Southeast), it was observed a considerable variation (31.76%) among the groups. The Fst ... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre

Resumo: Taenia saginata representa uma ameaça à segurança alimentar e à saúde pública devido à infecção pela ingestão de carne mal cozida e contaminada. Esta zoonose está amplamente distribuída, afetando humanos, os hospedeiros definitivos, e bovinos, hospedeiros intermediários. Além disto, a cisticercose bovina é responsável por perdas econômicas significativas devido à condenação de carcaças infectadas. A estratégia fundamental para o controle do complexo teníase-cisticercose consiste em interromper o ciclo evolutivo do parasita, evitando assim a infecção nos animais e no homem. Assim, a principal medida praticada no Brasil tem sido a inspeção de carcaças durante o abate, a qual é também a forma mais comum de diagnóstico. A insuficiente informação molecular de T. saginata tem dificultado o avanço das pesquisas para o aprimoramento de testes diagnósticos, o desenvolvimento de vacinas e a identificação de novas drogas para tratamento. Com o intuito de adquirir informação sobre o estágio de desenvolvimento metacestóide do parasita, foi utilizada a tecnologia de RNAseq para a montagem do transcriptoma de metacestóide de T. saginata. Estes dados serão úteis para estudos futuros envolvendo triagem para diagnóstico e marcadores imunoprofiláticos para a cisticercose bovina / Abstract:Taenia saginata represents a threat to food security and public health in consequence of human infection by ingestion of contaminated undercooked meat. This zoonosis is worldwide distributed, affecting human, definitive host, and bovine, intermediate host. Besides, bovine cysticercosis is responsible for significant economic losses due to the condemnation of infected carcasses. The main strategy to control taeniasis-cysticercosis complex consists of interrupting the parasite's biological cycle, thus preventing human and animal infection. Therefore, in Brasil the main control measure has been the carcass inspection during the slaughter, which is also the most common diagnostic practice. Insufficient T. saginata molecular information makes difficult consistent advances to the improvement of diagnostic tests, vaccine development and the identification of new drugs for treatment. In order to gain insights about the parasite's metacestode developmental stage, RNAseq technology was used to assemble the whole transcriptome of a T. saginata metacestode. These data will also be useful for the next generation screening studies of diagnostic and immunoprophylatic markers for bovine cysticercosis / Orientador:Cáris Maroni Nunes / Banca:Adam Taiti Harth Utsunomiya / Banca:Flávia Lombardi Lopes / Banca:Guilherme de Paula Nogueira / Banca: Daniel Guariz Pinheiro / Banca:Marcelo Vasconcelos Meireles / Doutor