Chromosome-level haplotype-resolved genome assembly of the linguliform brachiopod Discradisca antillarum (d'Orbigny,...

Brachiopods are a group of shelled, filter-feeding marine invertebrates. Though they superficially resemble bivalve mollusks, brachiopods fall within the clade Lophophorata (Brachiopoda, Bryozoa, Phoronida) and possess an abundant and diverse fossil record spanning more than 500 million years. This long evolutionary history makes Brachiopoda particularly important for understanding the evolution of the morphologically disparate superphylum Lophotrochozoa. Brachiopods also stand to provide insight into the evolution of biomineralization, as most lineages produce skeletons of calcium carbonate while linguliforms use calcium phosphate. However, genomic resources for brachiopods are limited. To enable comparative and evolutionary genomic studies of this clade, we generated a chromosome-level assembly for the discinid brachiopod Discradisca antillarum. Sequencing was performed using PacBio HiFi and Hi-C to produce both a primary (N = 8) and haplotype-resolved (2N = 16) assembly. The primary assembly comprises 208 scaffolds with the 8 chromosome-level scaffolds representing 96.6% of the genome. The primary assembly has a BUSCO genome completeness score of 95.5% (94.4% single copy, 1.0% duplicated, 0.9% fragmented). Annotation of protein-coding genes yielded 29,208 genes with a BUSCO protein completeness score of 95.6% (87.6% single copy, 8.0% duplicated, 2.8% fragmented). Comparative synteny between D. antillarum and other lophotrochozoans shows that, at the macrosyntenic level, the genome conserves all proposed ancestral lophotrochozoan fusion-with-mixing events while also revealing new fusions involving several bilaterian ancestral linkage groups. The genome of D. antillarum will enable significant insights into brachiopod evolution.