ArticleGenome biology and evolution2019
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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68 citing papers in PubMed, 127 citations in OpenAlex.
- Regional signaling controls stem cell-mediated regeneration in an invertebrate chordate.PLoS biology · 2026Article
- Using CRISPR/Cas9 to investigate the role of candidate human disease gene orthologs in Ciona.bioRxiv : the preprint server for biology · 2026Article
- Similarities betweeneNeuro · 2026Article
- Unique Tunicate Traits Possibly Encoded by Horizontally Transferred Genes.Genome biology and evolution · 2026Article
- An Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.Scientific data · 2026Article
- Tunicates have a complex, highly dynamic TNF superfamily.PloS one · 2026Article
- Divergence of immune cell types in chordate blood.Current biology : CB · 2025Article
- Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.The EMBO journal · 2025Article
- Genomic Insights Into Early-Stage Selective Filtering During the Transport Stage of Biological Invasions.Evolutionary applications · 2025Article
- Complementary Roles of DNA Methylation and miRNA in Regulating Gene Expression Under Environmental Stress in Biological Invasions.Evolutionary applications · 2025Article
- The dorsal/ventral subdivision of the hindbrain predates the tunicate/vertebrate split.bioRxiv : the preprint server for biology · 2025Article
- A gene regulatory network for specification and morphogenesis of a Mauthner Cell homolog in non-vertebrate chordates.Developmental biology · 2025Article
- Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3.Journal of molecular evolution · 2025Article
- Immune cell type divergence in a basal chordate.bioRxiv : the preprint server for biology · 2025Article
- First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata).GigaScience · 2025Article
- Redefinition of the toll-like receptor repertoire inFrontiers in cellular and infection microbiology · 2025Article
- Fine-Tuned Expression of Evolutionarily Conserved Signaling Molecules in theInternational journal of molecular sciences · 2024Article
- Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network.Integrative and comparative biology · 2024Review
- Article
- A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates.Development (Cambridge, England) · 2024Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.
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