An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi

Ciona savignyi is an important model organism across multiple disciplines, including developmental biology, ecology, evolution, and invasion science, and has become increasingly valuable for elucidating the genomic basis of adaptation in a rapidly changing world. Here, we present an improved chromosome-level genome assembly of C. savignyi, generated using a combination of Illumina short-read sequencing, Oxford Nanopore long-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C). The final assembly spans 200.63 Mb, with a contig N50 of 1.66 Mb and a scaffold N50 of 14.37 Mb, successfully anchored to 13 chromosomes. Interestingly, despite the compact genome, approximately 45% of the genome consists of repetitive sequences. We predicted 15,327 protein-coding genes, of which 96.2% were functionally annotated. This assembly substantially improves the quality and completeness relative to the previous version and represents one of the most contiguous ascidian genomes assembled to date. This genomic resource provides an essential resource for future research using C. savignyi as a model in multiple disciplines.