Life Through the Hologenome Window
Tom Gilbert
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen. Copenhagen, Denmark.
It is increasingly clear that symbiotic microbes not only benefit their eukaryotic hosts through food conversion and nutrient uptake, but they can also have broader effects on their hosts’ morphology, health, and even behavior. They are no longer considered passive passengers but active crew, who can affect and even condition phenotypes in complex organisms, whether plants, invertebrates, or vertebrates. The extent of these effects is so great, that although the two parties have traditionally been studied independently, a new “hologenomic” approach is now being embraced by the genomics community, that jointly analyzes the interconnection between host genomes and microbial metagenomes, and their combined functions. This is now feasible because the genomic revolution enables the generation of multi omics-scale data sets and analysis using novel data-mining methods. Indeed, recent research has showcased the feasibility of applying hologenomics to questions of ecological and evolutionary relevance. Therefore, there is a pressing need to understand how the evolution of complex host organisms is shaped by their associated microbes. Furthermore, now is the time to explore their broader implications in the context of fundamental ecological and evolutionary processes, grand transitions of life, and the history of humans – all topics that are typically attributed to other host-centric features such as genomic variation.
The Tempo of Virus Evolution
Katrina Lythgoe
Big Data Institute, University of Oxford. Oxford, UK.
Viruses replicate and evolve within the hosts that they infect, but sooner or later they need to transmit if they are going to survive in the long term. This can create evolutionary trade-offs, because what makes a virus fit within a given individual does not necessarily make it good at transmitting. On the other hand, within-host evolution might facilitate evolutionary ‘leaps’ that make the virus even fitter at the between-host level. I will explore how these processes can affect the tempo of viral evolution in human viruses, including HIV and SARS-CoV-2.
Population-scale sequencing of Drosophila melanogaster and Anopheles coluzzii uncovers transposable element contribution to gene expression variation and adaptive evolution
Josefa González
Evolutionary and Functional Genomics Laboratory, Institute of Evolutionary Biology (CSIC-UPF). Barcelona, Spain.
How organisms adapt to the environment is still an open question in Biology. Short read genome sequencing has allowed to explore the role of single nucleotide polymorphisms (SNPs) in environmental adaptation. However, SNPs alone can only explain a fraction of the existing ecologically relevant phenotypic variation. Among the structural variants that can now be studied thanks to the availability of long-read sequencing, transposable elements are likely to play a major role in adaptation due to their capacity to generate mutations that often have phenotypic effects of a complexity that is not achievable by point mutations. In our lab, we are studying the role of transposable elements in adaptation in the fruitfly Drosophila melanogaster and in the malaria vector Anopheles coluzzii. D. melanogaster is an excellent model species to quantify the role of transposable elements in environmental adaptation as it has recently colonized very distinct environments. We have generated 32 new D. melanogaster reference genomes using long-read sequencing of natural populations collected in arid, cold and temperate environments. We have discovered thousands of new transposable element insertions including copies from three new families. We have also generated transcriptomic data for 18 of these genomes, which is allowing us to elucidate the role of transposable elements in expression quantitative trait loci (eQTL) variation. In Anopheles species we are focusing on the potential role of transposable elements in urban adaptation. Based on the long-read sequencing of six larvae collected in urban breeding sites, we have generated the most comprehensive transposable element annotation in this species to date. This annotation has allowed us to identified several insertions that could potentially impact both genome architecture and the regulation of vectorial capacity genes. Overall, our results show that transposable elements contribute to gene expression variation and adaptive evolution.