A Chromosome-level Assembly and Functional Genomic Resources for the Model Annelid <i>Capitella teleta</i>

The polychaete Capitella teleta is a primary model for evolutionary developmental biology, comparative genomics, conservation, and ecotoxicology. Although it was the first polychaete genome sequenced, the original assembly is outdated by modern standards. Here, we combine long-read and short-read sequencing with Hi-C chromatin conformation capture to assemble chromosome-level nuclear and mitochondrial genomes of the laboratory strain of C. teleta. This reference assembly accurately reflects the expected genome size (∼243.6 Mb) and contains a highly complete, evolutionarily conserved gene repertoire. Notably, the nuclear and mitochondrial genomes are heavily rearranged, indicating a decoupling between gene family repertoire and chromosomal evolution. The analyses of developmental time courses of bulk and single-cell RNA-seq, ATAC-seq, and EM-seq data using the new reference assembly resulted in a significant improvement in quality, enabling the identification of new cell-type-specific gene markers. Finally, we generated a publicly available genome browser that ensures these resources comply with FAIR principles. Our study provides state-of-the-art genomic resources for C. teleta, addressing a pressing community need and opening new research opportunities in animal and genome evolution.