Ascidians are invertebrate chordates with different modes of reproduction and solitary vs. colonial organization, as well as diverse genomes, morphological features, and regenerative capacities. The botryllid clade of ascidians are a growing model for coloniality, whole body regeneration, immune function, genome expansion, and the evolution of these traits. This study implements a hybrid assembly technique with cost-effective sequencing to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp and a BUSCO score of 96.1\%. Genome annotation identified ~13,000 protein coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. We assembled and annotated the first genome for the colonial ascidian Botrylloides violaceus. This genome supports the use of economical genomic data from non-model organisms in the investigation of biological phenomena.

Modern genome sequencing technologies open new avenues for research on biological processes in non‐model organisms. Colonial ascidians are a diverse group of invertebrate chordates capable of whole body regeneration, an unusual trait that is absent from vertebrates. Although genomic data are available for a few related species, there exist no such data for the highly regenerative species Botrylloides violaceus. Using a de novo hybrid assembly approach, we present the first draft of the B. violaceus genome sequence. By integrating short read and long read sequencing technologies, genome assembly becomes cost‐effective and easily accessible. Comparative genomic analysis between B. violaceus and other chordate genomes reveals insights into the evolution of gene families implicated in regeneration and development. Support or Funding Information Warren J. Baker and Robert D. Koob Endowments, California Polytechnic State University; The Frost Fund, College of Science and Mathematics, California Polytechnic State University

Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from non-model organisms in the investigation of biological phenomena.