Periodic Reporting for period 2 - METASCALE (Modes of genome evolution during major metazoan transitions)
Reporting period: 2023-01-01 to 2024-06-30
• What is the problem/issue being addressed?
First animals appeared on the planet at least 700 million years ago. Some key early comparative genomic studies have identified a very complex set of genomic features that have persisted since then. The first big gap towards understanding this “genome architecture” was the absence of genome assemblies with fully resolved chromosomes. Over the past years, access to this information has revealed striking similarities among animal genomes at both chromosomal and sub-chromosomal levels. The current major focus is to understand whether this genome architecture is employed in similar or different ways across major animal clades.
• Why is it important for society?
Understanding past evolutionary trajectories of major animal clades is of primarily interest because this allows us to reconstruct the genomes of the first animals. This information also allows to understand changes within genes, regulatory regions, and whole chromosomes in these genomes. One of the outcomes of this particular project is the attempt to test whether animal genomes of different animal clades evolve along particular and non-interchangeable trajectories. If this is the case, then quantification of such trajectories will be crucial in the understanding of the evolutionary potential still harbored wihin each animal genome.
• What are the overall objectives?
In this project, we utilize the latest comparative and regulatory genomics approaches to study: (a) genome architecture evolution simultaneously at various evolutionary levels (both chromosomal and sub-chromosomal levels), and (b) using cephalopod mollusks as a model of a unique and clearly defined evolutionary trajectory we investigate how chromosomal and sub-chromosomal organizational principles are reflected in the modalities of their gene regulation.
First animals appeared on the planet at least 700 million years ago. Some key early comparative genomic studies have identified a very complex set of genomic features that have persisted since then. The first big gap towards understanding this “genome architecture” was the absence of genome assemblies with fully resolved chromosomes. Over the past years, access to this information has revealed striking similarities among animal genomes at both chromosomal and sub-chromosomal levels. The current major focus is to understand whether this genome architecture is employed in similar or different ways across major animal clades.
• Why is it important for society?
Understanding past evolutionary trajectories of major animal clades is of primarily interest because this allows us to reconstruct the genomes of the first animals. This information also allows to understand changes within genes, regulatory regions, and whole chromosomes in these genomes. One of the outcomes of this particular project is the attempt to test whether animal genomes of different animal clades evolve along particular and non-interchangeable trajectories. If this is the case, then quantification of such trajectories will be crucial in the understanding of the evolutionary potential still harbored wihin each animal genome.
• What are the overall objectives?
In this project, we utilize the latest comparative and regulatory genomics approaches to study: (a) genome architecture evolution simultaneously at various evolutionary levels (both chromosomal and sub-chromosomal levels), and (b) using cephalopod mollusks as a model of a unique and clearly defined evolutionary trajectory we investigate how chromosomal and sub-chromosomal organizational principles are reflected in the modalities of their gene regulation.
The team has developed all the necessary bioinformatic and experimental approaches as outlined in the proposal, starting from inclusion of the graph database format, to multi-level homology structure investigation and analysis, and experimental procedures on genome topology and gene regulation in the Hawaiian bobtail squid E. scolopes. After publishing several papers on the chromosomal “algebra” characterization and potential sub-chromosomal evolutionary effects, the team is now approaching a phase of a second major set of publications.
Our main ongoing goal are three major papers:
(1) Generalized chromosomal algebra and chromosomal and sub-chromosomal scales, FWM dynamics and regulatory implications (Schultz et al, in preparation/submission)
(2) Impact of ancient cephalopod rearrangements on the emergence of novel functional gene linkages (Rogers et al, in preparation)
(3) Emerging vision of animal genomic landscape as an expanding/contracting coordinate system, with description of an experimental assessment of these processes. (Kon et al, in preparation/submission)
We think that these papers, if successful, will establish “evolutionary topology” as a system to classify and study macro-evolutionary changes within animal genomes.
(1) Generalized chromosomal algebra and chromosomal and sub-chromosomal scales, FWM dynamics and regulatory implications (Schultz et al, in preparation/submission)
(2) Impact of ancient cephalopod rearrangements on the emergence of novel functional gene linkages (Rogers et al, in preparation)
(3) Emerging vision of animal genomic landscape as an expanding/contracting coordinate system, with description of an experimental assessment of these processes. (Kon et al, in preparation/submission)
We think that these papers, if successful, will establish “evolutionary topology” as a system to classify and study macro-evolutionary changes within animal genomes.