TRANSPOSE: Transposable elements as agents of genome evolution and adaptation following a recent whole genome duplication

Transposable elements (TEs) are abundant, mobile DNA sequences whose behavior can have profound evolutionary impacts. Often seen as selfish genetic elements, recent research has shown TEs can modify gene regulation and drive structural rearrangements of genomes. Salmonid fishes are an excellent system to explore the role of TEs and other types of repetitive DNA in genome evolution and the creation of adaptive innovations. Species vary in the quantity and diversity of DNA repeats, and interspecies comparisons reveal how they reshape genomes and gene regulatory networks over time. In addition, these fishes have undergone adaptive divergence and radiation in many species following a recent whole genome duplication event. This genome duplication enables us to explore mechanistic links between DNA repeats and the architecture of genomes. Finally, salmonids have a novel sex chromosome system with a jumping repeat-encapsulated male determining gene, making them a excellent group of species to understand the role of repetitive DNA in sex chromosome evolution and the resolution of sexual conflict. To understand the role of repetitive DNA in genome evolution, the TRANSPOSE project has created 34 high-quality genome assemblies from 14 different species of salmonid fishes using cutting edge long read sequencing technology; Atlantic salmon, brown trout, rainbow trout, coho salmon, Arctic charr, Whitespotted char, Danube salmon, Siberian taimen, Sakhalin taimen, Lenok spp., grayling, Amur grayling, lake whitefish and Bonneville Cisco. For Atlantic salmon we constructed the first pan-genome, a composite representation of the salmon genome constructed from the high-quality assemblies of 11 individuals sampled across the species range. This pan-genome represents a hugely improved reference compared to previous genomic resources and is essential to perform in-depth characterization of structural variants (SVs) in Atlantic salmon. The pan-genome was analyzed with novel methods that detected >1 million SVs and encompassing 367 Mb of sequence, equivalent in size to ~3 whole chromosomes. Many of these SVs overlapped the coding sequence of genes, indicating that they directly affect gene functions. Association tests using 366 wild salmon sequenced with short-read technology and graph-genome analyses detected multiple SVs contributing to environmental adaptation. The salmon pan-genome was also used to detect multiple large inversions in Atlantic salmon and investigate the mechanisms leading to supergene formation and to characterize the repeat DNA flanking the salmon sex-determining gene (sdY). Comparison and repeat annotation of the sex determining region on three different chromosomes in Atlantic salmon detected large species-specific repeat expansions that were shared between non-homologous chromosomes. This suggests that ectopic recombination facilitated by repeats is the mechanism by which sdY moves among chromosomes. For rainbow trout, we constructed a high-quality genome assembly that allowed us to discover a large (54Mb) double inversion (supergene) that contains several life-history related genes. This inversion influences the propensity to undergo sex-biased marine migration. For lake whitefish from North America, (Coregonus clupeaformis), we generated high-quality genome assemblies for a sympatric species pair of ‘Dwarf’ and ‘Normal’ ecotypes, revealing that SVs may play an important role in differentiation and speciation in the absence of geographical barriers to interbreeding. Analysis of interactions between gene regulation and transposable elements revealed that gene duplicate copies that had evolved lower gene expression across most tissues following the whole genome duplication had higher TE insertion rates in gene promoters. We found that 20% of cis-regulatory elements, i.e., those next the genes they control, were derived from TEs and that there had been a stronger selection against TE-derived cis-regulatory elements in brain. Using reporter assays we showed that many TEs impact transcription with old long-terminal repeat TEs being enriched for gene regulatory activity compared to other types of TEs. Finally, we found that TEs have significantly impacted the evolution of gene regulatory networks in salmon, but surprisingly most of the regulatory evolution related to TE activity happened prior to the salmonid whole genome duplication event.

The TRANSPOSE project has generated results that are of interest to the wider community beyond salmonid research and have been disseminated in top open access peer-reviewed scientific journals that satisfy FAIR requirements. TRANSPOSE has provided a step-change in salmonid genomic resources, including construction of high-quality assemblies and pan-genomes, as well as characterization and annotation of SVs and large inversion supergenes. These resources accelerate a transition away from the use of linear reference genomes for the global salmonid research community and open-up as yet untapped possibilities for understanding, for example, how genotypes are translated to phenotypes and fundamentally how populations and genomes evolve. The pan-genome and identification of SVs for Atlantic salmon are of direct relevance to conservation managers and stakeholders in wild salmon and salmon industries. TRANSPOSE has also contributed extensive new functional genomics dataset for salmonid species, including RNA-Seq and ATAC-Seq in different tissues and stages of ontogeny, which will be shared with the research community via the European AQUA-FAANG project that Lien coordinates. All the results and raw data generated in this project have been made publicly available through open access publications and/or deposition of data to international databases such as ENA and array-express. Genomic resources have also been made available through the salmobase.org infrastructure (www.salmobase.org).

In recent years, transposable elements (TEs) have emerged as key factors affecting genome regulation. A pressing challenge now is to understand the biological consequences of TEs reshaping the genome: how important are TEs as sources of adaptive innovations, and what are the long-term implications of TE-activity in eukaryote evolution? To answer these questions we need to (i) construct highly contiguous genome assemblies that fully incorporate repetitive TEs and (ii) use computational and experimental approaches to evaluate adaptive biological effects of TE-derived evolutionary innovations. Excitingly, with the evolution of single-molecule long-read sequencing, novel computational methods to distinguish adaptive and neutral innovations in genome regulation, and the opportunities CRISPR/Cas9 brings for functional validation, these past challenges and limitations can now be addressed. TRANSPOSE will use salmonid fishes, which have a high load of TEs in their genome, as a model system to understand the functional roles of TEs in vertebrate evolution. We will explore how TEs have shaped 1) rediploidization following the salmonid whole genome duplication, 2) remodeling of gene expression evolution, 3) micro-rearrangements and local adaptation, and 4) the evolution of dynamic sex chromosome systems. Using cutting-edge long-read sequencing technology to generate reference genome assemblies for 11 salmonid lineages and 2 outgroup species, we will resolve the importance of TE-mediated structural chromosome evolution to adaptive evolution, determine the role of translocations in adaptive divergence and identify the drivers of dynamics of sex chromosome turnover. In addition, we will generate extensive functional omics datasets and apply novel computational methods in an explicit phylogenetic framework to bridge the gap between TEs, genome evolution and the evolution of gene regulation. TRANSPOSE will significantly advance our understanding of how TEs matter.