Genômica comparativa de protozoários

Made available in DSpace on 2016-04-12T12:41:56Z (GMT). No. of bitstreams: 2 diogo_tschoeke_ioc_dout_2013.pdf: 6504204 bytes, checksum: 8ee03e5b054b7754e81ce9d1e278efee (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2013Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilOs protozoários são definidos como organismos eucariotos unicelulares, e apresentam grande diversidade e variedade. Cerca de 200 mil espécies são descritas e quase 10.000 são parasitas. As espécies patogênicas causam doenças como a malária, doença do sono, doença de Chagas, leishmaniose, amebíase e giardíase. Portanto, estudos comparativos entre os protozoários são importantes porque estes podem mostrar semelhanças e diferenças entre essas espécies. A identificação de ortólogos é importante para a categorização funcional de genomas, porque ortólogos tipicamente ocupam o mesmo nicho funcional nos diferentes organismos, enquanto a identificação de parálogos é importante porque eles são submetidos a uma diversificação funcional via duplicação, através dos processos de neofuncionalização e subfuncionalização. A fim de realizar uma análise comparativa de 22 protozoários, 204.624 proteínas não redundantes de Plasmodium, Entamoeba, Trypanosoma, Leishmania, Giardia, Theileria, Toxoplasma, Trichomonas e Cryptosporidium, foram submetidos ao programa OrthoMCL, resultando em 26.101 grupos homólogos. Entre eles, 21.119 grupos são ortólogos, incluindo 7.679 co-ortólogos (grupos que contêm parálogos recentes), e 4982 são parálogos internos. Entre os ortólogos, 348 são compartilhados por todas as 22 espécies e representam o núcleo proteômico de Protozoa Com este núcleo realizamos uma análise filogenômica, usando os 348 ortólogos concatenados, resultando em uma supermatriz de 328.228 posições, que geraram uma árvore de espécies para os 22 protozoários. Quando inferimos os diferentes Núcleos Proteômicos, Kinetoplastida tem 5.000 grupos ortólogos e 67,92 % (3396/5000) são Kinetoplastida específicos, além disso, 46,29% (1592/3396) destes ortólogos são anotados como "hipotéticos". O núcleo proteômico de Apicomplexa tem 986 grupos ortólogos e 27,82% (224/986) são específicos, enquanto que 40,63% (92 /224) destes são classificados como hipotéticos. O núcleo proteômico de Entamoeba tem 5.915 grupos ortólogos e 75,08% (4441/5915) destes grupos são específicos, sendo que 65,41% (2905/4441) são anotados como hipotéticos. Analisando os parálogos, Trichomonas vaginalis foi a espécie que apresentou o maior número de grupos parálogos internos, 2933, e também mostrou 948 co-ortólogos totalizando 3.881 parálogos. Um aprofundamento da análise na ordem Kinetoplastida mostrou que Trypanosoma cruzi apresenta o número mais elevado de duplicações, totalizando 5.777 parálogos, sendo 4963 co-ortólogos e 814 parálogos internos Os resultados da montagem e análise de L. amazonensis resultaram 29.670.588 bases e 8802 CDS identificadas. A análise comparativa do gênero Leishmania mostrou que as seis espécies estudadas compartilham 7016 ortólogos, enquanto L. amazonensis e L. mexicana têm o maior número de ortólogos-específicos e L. braziliensis o maior número de paralogos internos. A análise filogenômica mostrou a posição taxonômica esperada de L. amazonensis e juntamente com L. mexicana formando o "complexo Mexicana", além da separação esperada do subgênero Leishmania. Encontramos potenciais proteínas análogas entre L. amazonensis e Homo sapiens e dentro do genoma de L. amazonensis, denominados análogos intragenômicos. Finalmente, a mineração por genes de RNAi mostrou que L. amazonensis , provavelmente não apresenta esta via funcionalProtozoa are defined as single celled eukaryotic organisms showing an extremely diversity and variety. Approximately 200,000 species are described and nearly 10,000 are parasitic. The pathogenic species cause diseases such as malaria, sleeping sickness, Ch agas disease, leishmaniasis, amoebiasis and giardiasis. Therefore, comparative studies among Protozoa are important because they may identify similarities and differences in these species. Orthologs identification is central to functional characterization of genomes because orthologs typically occupy the same functional niche in different organisms, while paralogs identification is important because they undergo a functional diversification by duplication, via the processes of neofunctionalization and subfu nctionalization. In order to perform comparative protozoa analysis, 204,624 non - redundant proteins from Plasmodium , Entamoeba , Trypanosoma , Leishmania , Giardia , Theileria , Toxoplasma , Trichomonas and Cryptosporidium , totalizing 22 species, were submitted t o OrthoMCL resulting in 26,101 homologs groups. Among them, 21,119 groups are orthologs including 7,679 co - orthologs (groups that contain recent paralogs) and 4,982 are inparalogs. Among the orthologs, 348 are shared by all 22 species, representing the Pro tozoa core proteome, with this core we perform ed a phylogenomic analysis with the 348 concatenated orthologs, resulting in a global supermatrix of 328,228 positions that generate a species tree for the 22 protozoa. When we inferred Core Proteome, the Kinet oplastida core has 5,000 orthologous groups and 67.92% (3,396/5000) are Kinetoplastida Specific, besides 46.29% (1,592/3,396) of these orthologs are annotated as “hypothetical”. Apicomplexa Core Proteome has 986 orthologous groups and 27.82% (224/986) are Apicomplexa Specific whereas 40.63% (92/224) were classified as hypothetical proteins. Entamoeba Core Proteome has 5,915 orthologous groups and 75.08% (4,441/5,915) of these groups are Entamoeba Specific and 65.41% (2,905/4441) were annotated as hypothetic al. Analyzing the paralogs, Trichomonas vaginalis was the specie s that presented the highest number of inparalogs groups, 2,933 and also showed 948 co - orthologs totalizing 3881 paralogs. A deep look into the Kinetoplastida order showed that Trypanosoma cruzi has the highest duplication number, totalizing 5777 paralogs, 4963 co - orthologs and 814 inparalogs groups . The L. amazonensis analysis resulted in 29,670,588 bases assembled, and 8802 CDS identified. Comparative analysis into the Leishman ia genus showed that these 6 species share 7016 ortologs, whilst L. amazonensis and L. mexicana has the biggest number of specific orthologs and L. braziliensis biggest number of inparalogs. Phylogenomic analysis showed the expected L. amazonensis taxonomi c position together with L. mexicana forming the “Mexicana complex” and the New and Old Leishmania (L . ). spp. separation. Potential analagous proteins were found between L. amazonensis and H omo sapiens , and also into the L. amazonensis proteome. Finally, R NAi analysis showed that L. amazonensis , probably, do not have functional RNAi pathwa

ProtozoaDB 2.0: A Trypanosoma Brucei Case Study

Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2.0, now with the genomes of 22 pathogenic Protozoa. The system has been fully remodeled to allow for new tools and a more expanded view of data, and now includes a number of analyses such as: (i) similarities with other databases (model organisms, the Conserved Domains Database, and the Protein Data Bank); (ii) visualization of KEGG metabolic pathways; (iii) the protein structure from PDB; (iv) homology inferences; (v) the search for related publications in PubMed; (vi) superfamily classification; and (vii) phenotype inferences based on comparisons with model organisms. ProtozoaDB 2.0 supports RESTful Web Services to make data access easier. Those services were written in Ruby language using Ruby on Rails (RoR). This new version also allows a more detailed analysis of the object of study, as well as expanding the number of genomes and proteomes available to the scientific community. In our case study, a group of prenyltransferase proteinsalready described in the literature was found to be a good drug target for Trypanosomatids

Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus

Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages

Additional file 3: Table S3. of Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

Adonis (PERMANOVA) results of taxonomic composition of AF metatranscriptomics (XLSX 11 kb

Additional file 1: Table S1. of Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

Similarity count table of sequences classified as Spirometra. (XLSX 14 kb

Additional file 2: Table S2. of Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

Multiple T Teste performed comparing the diversity index (Shannon and Simpson) between AF Zika samples and Controls Groups. (XLSX 11 kb

Dissecting light sensing and metabolic pathways on the millimeter scale in high-altitude modern stromatolites

Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin–Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood–Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.EEA RafaelaFil: Alonso-Reyes, Daniel Gonzalo. Universidad Nacional de Tucumán. Centro Integral de Microscopía Electrónica (CIME). Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Alonso-Reyes, Daniel Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Integral de Microscopía Electrónica (CIME). Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Alonso-Reyes, Daniel Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI). Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas; ArgentinaFil: Galván, Fátima Silvina. Universidad Nacional de Tucumán. Centro Integral de Microscopía Electrónica. Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Galván, Fátima Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Integral de Microscopía Electrónica. Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Irazoqui, Jose Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación de la Cadena Láctea; ArgentinaFil: Irazoqui, Jose Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea; ArgentinaFil: Amadio, Ariel​. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea; ArgentinaFil: Amadio, Ariel​. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación de la Cadena Láctea; ArgentinaFil: Diogo Tschoeke. Federal University of Rio de Janeiro. Institute of Biology and Coppe; BrasilFil: Fabiano Thompson. Federal University of Rio de Janeiro. Institute of Biology and Coppe; BrasilFil: Albarracín, Virginia Helena. Universidad Nacional de Tucumán. Centro Integral de Microscopía Electrónica (CIME). Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Albarracín, Virginia Helena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Integral de Microscopía Electrónica (CIME). Laboratorio de Microbiología Ultraestructural y Molecular; ArgentinaFil: Albarracín, Virginia Helena. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Farias, María Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI). Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas; Argentin