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Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/209220
An Omics World: Colonization and Adaptive Processes of Styela plicata
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[eng] In the last decades biological invasions have emerged as a global concern, as they impact local biodiversity by disrupting ecosystem functioning and ultimately affect human health, economy and wellness. In a climate change scenario, catalyzed by globalization, the issue of invasive species is expected to become magnified in the near future. However, little is known about the intrinsic mechanisms allowing invasive species to overcome new conditions and become a major threat worldwide. This PhD thesis aims to study the colonization and adaptive processes of the invasive tunicate S. plicata worldwide using ‘-omic’ approaches, including population genomics and microbiome. By combining multiple sequencing techniques such as PacBio Long Reads, Illumina Whole Genome Sequencing (WGS), Illumina RNAseq and Illumina amplicon sequencing, we have adopted multiple approaches to the study of this species. First, by using 80 publicly available genomes, we evaluated general output trends when using the 2b-RADseq technique depending on the genomic architecture of target species, demonstrating that overall the technique does not generate biases although it slightly enriches exonic regions. Furthermore, by empirically testing the effect of 2b-RADseq base-selective adaptors on genotyping using four S. plicata individuals, we paved the way for cost-effective population studies on this species. Next, we built and annotated a “de-novo” reference genome for S. plicata, and combined it with Illumina WGS of 24 individuals worldwide. The resulting pangenome revealed the presence of 4 potentially adaptive inversions, the first evidence of population structure, SNPs related to local adaptation, and mito-nuclear interactions. These methodological improvements and the generation of a reference genome assembly allowed us to analyze 87 individuals from 18 localities worldwide using 2b-RADseq to further reveal its population genomic structure, finding clear signals of local adaptation and recent demographic bottlenecks related to invasive events. Finally, using Illumina sequencing of the V4 region of the 16S gene of several tissues of juvenile and adult individuals and water samples from three harbors, in addition to adult samples on two of these harbors over two years, we shed light on the dynamics of the microbiome hosted by S. plicata. We revealed that Methylocaeanibacter sp. ASV0 is the most important bacteria in the tunic, whereas Gammaproteobacteria ASV1 and the unidentified bacteria ASV2 are so in the gill for holobiont survival. Moreover, we found evidence of abundance shifts through adulthood for these bacteria, suggesting active enrichment by S. plicata towards its symbiotic bacterial community. Finally, we revealed potential adaptive bacteria responding to seasonality and trace elements such as Candidatus Hepatoplasma sp. ASV11 and Endozoicomonas sp. ASV50, among others. This multilevel approach provides a solid basis to properly understand the mechanisms of Styela plicata and other invasive marine species to colonize and quickly adapt to new habitats.
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GALIÀ CAMPS, Carles. An Omics World: Colonization and Adaptive Processes of Styela plicata. [consulta: 28 de novembre de 2025]. [Disponible a: https://hdl.handle.net/2445/209220]