BRIDGING FUNCTIONAL AND PHYLOGENETIC DIVERSITY OF MARINE HETEROTROPHIC PROTISTS VIA SINGLE-CELL TRANSCRIPTOMICS

The comprehensive description of unicellular heterotrophic protists is essential for understanding the functioning of marine ecosystems and defining evolutionary relationships within marine microbial communities. For that reason, new insights into the functional genes of key protists, such as ciliates and dinoflagellates, are needed to complement the increasing taxonomic complexity and bridge the gap between various eco-functional processes in the ocean. In this study, single-cell transcriptomic sequencing proved to be an efficient method to create a snapshot of expressed genes of unicellular heterotrophs. We sequenced 65 single-cell transcriptomes from 20 fresh field samples collected from Sub-Arctic and North Sea waters. These 13 ciliate and 52 dinoflagellate transcriptomes will generally contribute to a greater understanding of functional and evolutionary processes of these marine protists. Further, we generated multi-gene phylogenies of several dozen genes to unravel the relationships of these heterotrophic taxa to other dinoflagellates and ciliates, respectively. These approaches also helped to elucidate the evolution of functional genes and traits for these understudied essential groups. Additionally, the datasets were incorporated into our metatranscriptomic reference database to fill the gap (of approx. 50%) of genomic information of heterotrophic organisms and their functional processes. Overall, identifying the phylogenetic relationships and functional diversity of heterotrophic and mixotrophic protists will clarify paramount marine microbial food web processes and provide clues to the system's sensitivity to climate change

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Transcriptome analysis of single cells: a plankton characterization of Arctic waters

The functional and taxonomic diversity of marine protists in the Arctic is large and a scientifically underestimated source of biodiversity. However, this diversity is being masked in terms of environmental bulk sampling, just as it is done within population-averaged samples retrieved from pure cultures. Yet in recent years, low-input RNA-sequencing methods have been adapted to work with single cells. Thus, increasing the number of unicellular transcriptomes sequenced and deepening the knowledge about the species distribution as well as phylogeny based on functional data analysis pipelines. Within this thesis, the SMART-Seq v4 protocol by Takara Clontech was successfully applied to study single cells during the HE492 field trip in Arctic waters. Further, it greatly enabled the simultaneous processing of multiple protists around Spitsbergen. Altogether, 42 single cells have been processed with the SMART-Seq v4 protocol. Afterwards 21 samples were indexed according to the Illumina Nextera XT library preparation protocol and subsequently 20 individual cDNA libraries pooled for sequencing on the Illumina NextSeq 500 platform. After sequencing each transcriptome has been de novo assembled and annotated via the Trinotate processing pipeline. Overall, the thesis evaluates the work flow establishment regarding single cell transcriptomics as a tool for field sampling and analysis positively, as resulted sequence data could be promisingly functionally annotated. The results demonstrate the possibility to study single cells to quantify inter-population heterogeneity previously masked in bulk measurements and moreover the method bypasses the need of cell cultivation. Ultimately single cell approaches will open new analytical avenues for studying culture independent unicellular plankton species in terms of cell subtypes and gene expression dynamics even in remote areas

Resumos concluídos - Bioquímica

Resumos concluídos - Bioquímic

Resumos concluídos - Bioquímica

Resumos concluídos - Bioquímic