A nearly-complete genome of Ciona intestinalis type A (C. robusta) reveals the contribution of inversion to chromosomal evolution in the genus Ciona

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  • Satou, Yutaka
    Department of Zoology, Graduate School of Science, Kyoto University
  • Nakamura, Ryohei
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo
  • Yu, Deli
    Department of Zoology, Graduate School of Science, Kyoto University
  • Yoshida, Reiko
    Department of Zoology, Graduate School of Science, Kyoto University
  • Hamada, Mayuko
    Ushimado Marine Institute, Faculty of Science, Okayama University
  • Fujie, Manabu
    DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University
  • Hisata, Kanako
    Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
  • Takeda, Hiroyuki
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo
  • Satoh, Noriyuki
    Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
  • Rachel O’Neill
    editor

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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