A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Yutaka Satou, Ryohei Nakamura, Deli Yu, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh, Rachel O'Neill

Research output: Contribution to journalArticle

5 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)3144-3157
Number of pages14
JournalGenome biology and evolution
Issue number11
Publication statusPublished - Nov 1 2019



  • Ciona intestinalis type A (C. robusta)
  • ascidian
  • chromosomal inversion
  • genome

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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