Increased Sampling of Small-Bodied Lophotrochozoans Yields Enhanced Resolution of the Most Enigmatic Invertebrate Superphylum

Lophotrochozoa is a major animal superphylum encompassing 15 protostome phyla, displaying remarkable morphological and ecological diversity, yet relationships among its constituent phyla remain unresolved. As sequencing technology evolves, genomic sequencing has proven to be a powerful tool for studying animal evolution, including the evolution of ancient lineages such as those among Lophotrochozoa. However, many lineages within Lophotrochozoa are small-bodied and understudied, complicating sequencing and sampling for analyses of evolutionary relatedness and sequence evolution. Here, I develop and validate a workflow using multiple displacement amplification (MDA) to enable PacBio HiFi sequencing from picogram quantities of DNA from small-bodied animals. Using this approach, I produce the first genome of the gastrotrich Lepidodermella squamata, providing a framework for further genome sequencing of small-bodied organisms and assess the evolution of gene content and Hox gene organization in Gastrotricha. Second, I generate a chromosome-level genome assembly for the brachiopod Discradisca antillarum and use comparative macrosynteny to identify conserved chromosomal fusion-with-mixing events across lophophorate taxa, providing independent genomic evidence for relationships among Brachiopoda, and Bryozoa. Third, I reconstruct a transcriptome-based phylogeny of Entoprocta, and present genome-scale data from Barentsia sp., providing strong support for taxonomic revisions within the phylum. Lastly, I analyze sequences from representative Lophotrochozoan phyla to elucidate internal relationships within the superphylum.