Eukaryotic diversity through the lens of metabarcoding and metagenomics
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Ruiz Trillo, Iñaki
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309 p.
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Mitsi, K. Eukaryotic diversity through the lens of metabarcoding and metagenomics. 2021. handle: http://hdl.handle.net/10803/671809
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Programa de doctorat en Biomedicina
Abstract
Los organismos eucariotas abarcan una diversidad inmensa de formas, tamaños y estilos de vida. Sin embargo, abordar la verdadera amplitud de esa diversidad es una tarea laboriosa. Durante las últimas decadas, los estudios de biodiversidad han experimentado un progreso importante gracias a la incorporación de técnicas basadas en la secuenciación del ADN. Esta tesis es una composición de tres proyectos independientes donde estas técnicas se aplican con el objetivo de ampliar nuestro conocimiento de la biodiversidad eucariota. En el primer proyecto, obtenemos el genoma nuclear y el genoma mitocondrial de un parásito a partir de un metagenoma eucariota. Definimos la posición filogenética de este nuevo organismo que se posiciona junto con Filasterea, un grupo de organismos unicelulares que está estrechamente relacionado con los animales y es clave para estudiar la transición a la multicelularidad animal. El análisis del contenido génico muestra que el nuevo organismo posee un genoma reducido en comparación con los otros Filasterea. A pesar de eso, su genoma codifica un flagelo completo y muchas proteínas que están relacionadas con la multicelularidad en los animales. En el segundo proyecto, buscamos diversidad molecular no descrita dentro de los platelmintos, uno de los filos animales más diversos e importantes desde un punto de vista biomédico. Con este fin, analizamos datos globales de metabarcoding del gen 18S del ADN ribosomal procedentes de hábitats marinos y de agua dulce. Nuestros resultados muestran que gran parte de la diversidad molecular de los platelmintos sigue sin estar documentada e identifican los habitats de agua dulce como puntos donde buscar nuevas especies de platelmintos. Por último, en el tercer proyecto, investigamos la novedad a nivel molecular, la composición taxonómica y la estructura de la comunidad eucariota del lago Sanabria, un lago oligotrófico. Secuenciamos la región hipervariable V4 del gen 18S del ADN ribosmal y demostramos cómo la elección de los métodos analíticos (ASVs o OTUs) afectan los resultados y las conclusiones sacadas por un estudio de biodiversida.. En conjunto, nuestros resultados amplían nuestra perspectiva de la diversidad eucariota y mejoran nuestra comprensión de la distribución, la ecología, la novedad molecular y los rasgos genómicos de los eucariotas.
Eukaryotes encompass an unprecedented diversity of forms, sizes and lifestyles. However, tackling the real breadth of that diversity is a challenging task. In the last decades, the assessment of biodiversity has seen substantial progress due to the incorporation of culture-independent techniques based on Next Generation DNA Sequencing. This thesis is a composition of three independent projects that implement these techniques aiming to expand our understanding of the extant eukaryotic biodiversity. In the first project, we obtain the nuclear and mitochondrial genomes of Txikispora philomaios, an uncultured unicellular parasite, using a metagenomic approach. We define the phylogenetic position of T.philomaios that branches within Filasterea, a group of unicellular eukaryotes that is closely related to animals and is key to elucidate the transition to animal multicellularity. Despite T.philomaios possessing a reduced genome in comparison to other Filasterea, it has a complete flagellar toolkit and its genome encodes many proteins that are related to multicellularity in animals. In the second project, we seek undescribed molecular diversity inside the phylum Platyhelminthes, one of the most diverse and biomedically important animal phyla. To this end, we analyze global metabarcoding data of the 18S rDNA gene from marine and freshwater habitats. Our results show that a large part of the molecular diversity of Platyhelminthes remains undocumented and identify freshwater environments as potential reservoirs for novel species of flatworms. Finally, in the third project, we investigate the molecular novelty, the taxonomic composition and the structure of the eukaryotic community in Sanabria Lake by sequencing the V4 hypervariable region of the 18S rDNA gene. We show to which extent the choice of the analytical methods (ASVs or OTUs) affects the final results and conclusions of a biodiversity survey. Altogether, our results broaden our perspective of eukaryotic diversity and enhance our understanding of the distribution, the ecology, the molecular novelty and the genomic traits of eukaryotes
Eukaryotes encompass an unprecedented diversity of forms, sizes and lifestyles. However, tackling the real breadth of that diversity is a challenging task. In the last decades, the assessment of biodiversity has seen substantial progress due to the incorporation of culture-independent techniques based on Next Generation DNA Sequencing. This thesis is a composition of three independent projects that implement these techniques aiming to expand our understanding of the extant eukaryotic biodiversity. In the first project, we obtain the nuclear and mitochondrial genomes of Txikispora philomaios, an uncultured unicellular parasite, using a metagenomic approach. We define the phylogenetic position of T.philomaios that branches within Filasterea, a group of unicellular eukaryotes that is closely related to animals and is key to elucidate the transition to animal multicellularity. Despite T.philomaios possessing a reduced genome in comparison to other Filasterea, it has a complete flagellar toolkit and its genome encodes many proteins that are related to multicellularity in animals. In the second project, we seek undescribed molecular diversity inside the phylum Platyhelminthes, one of the most diverse and biomedically important animal phyla. To this end, we analyze global metabarcoding data of the 18S rDNA gene from marine and freshwater habitats. Our results show that a large part of the molecular diversity of Platyhelminthes remains undocumented and identify freshwater environments as potential reservoirs for novel species of flatworms. Finally, in the third project, we investigate the molecular novelty, the taxonomic composition and the structure of the eukaryotic community in Sanabria Lake by sequencing the V4 hypervariable region of the 18S rDNA gene. We show to which extent the choice of the analytical methods (ASVs or OTUs) affects the final results and conclusions of a biodiversity survey. Altogether, our results broaden our perspective of eukaryotic diversity and enhance our understanding of the distribution, the ecology, the molecular novelty and the genomic traits of eukaryotes
Keywords
Metabarcoding, Metagenomica, Protistas, Multicelularidad, Biodiversidad, Metagenomics, Protists, Multicellularity, Biodiversity
Subjects
575 - General genetics. General cytogenetics. Immunogenetics. Evolution. Phylogeny
