Neglected genomic elements in overlooked taxonomic groups: diversity, evolution, and genomic impact of transposable elements in bivalve molluscs

Transposable elements (TEs) are intriguing features found in all eukaryotic genomes, capable of replicating independently within the host cell and spreading throughout the genome. They exhibit high diversity across various eukaryotic clades and even among closely related species. While traditionally overlooked, advancements in long-read sequencing technologies have revitalized their study. However, their distribution, evolutionary trajectories, and biological consequences remain still poorly understood in non-model species. Bivalves (Class: Bivalvia), an ancient and diversified clade of filter-feeding molluscs, represent one of such overlooked taxonomic group. This dissertation makes a first attempt to addresses this gap by exploring the distribution, evolution, and genomic impacts of TEs across the clade. After generating a novel long reads-based genome assembly for the Manila clam Ruditapes philippinarum, I utilized a wide sampling of bivalve genomes to study the distribution and evolution of LINEs, SINEs, and DDE/D DNA transposons across their diversity. Bivalves were found to host a highly diversified TE complement compared to other molluscs, with multiple bivalve-specific amplifications likely associated with their diversification. Then I characterized the genomic impacts of TEs and related Structural Variants (SVs) among the economically important oysters. Here, I found that up to 14% of the oyster genome exhibits structural differences between haplotypes in terms of insertions and deletions. TEs and SVs were also found to be significant contributors to population differentiation in the Estuarine oyster Crassostrea ariakensis, potentially providing substrates for local adaptations to varying ocean salinity and temperatures. As a secondary outcome of these projects, I significantly increased the availability of high-quality TE resources for bivalves by depositing hundreds of novel sequences in freely available databases. The post-genomics era presents an unparalleled opportunity for scientists to understand genome composition and evolution and this dissertation might help further research into characterizing transposons and their effects in other non-model species.