TY - JOUR
T1 - A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
AU - Satou, Yutaka
AU - Nakamura, Ryohei
AU - Yu, Deli
AU - Yoshida, Reiko
AU - Hamada, Mayuko
AU - Fujie, Manabu
AU - Hisata, Kanako
AU - Takeda, Hiroyuki
AU - Satoh, Noriyuki
AU - O'Neill, Rachel
N1 - Funding Information:
We mapped Illumina sequencing data obtained from a previous study (Satou et al. 2015) (supplementary fig. S2B, Supplementary Material online) to examine whether these candidate positions were supported by paired-end sequences. Similarly, we mapped sequence data of both insert ends of BAC clones, which were derived from Sanger sequencing (Dehal et al. 2002; Kobayashi et al. 2002). For each of the candidates supported by any of these sequencing data, we inspected Hi-C data using the Hi-C data browser (Durand et al. 2016). As a result, we obtained a new set of 14 chromosomal sequences containing 95,495,880 bases. This set of chromosomal sequences was used as references for the new assembly (see below). Hereafter, these reference scaffolds are tentatively called KH/Hi-C linked scaffolds.
Funding Information:
We thank Chikako Imaizumi for technical help and Dr Steven Aird for English editing. This work was supported by grants from the Japan Society for the Promotion of Science (17KT0020 to Y.S., 16H04824 to N.S., and 18K14620 to R.N.) and from the Japan Science and Technology Agency (JPMJCR13W3 to H.T.). The inbred line was established under National Bio-Resource Project for Ciona intestinalis.
PY - 2019/11/1
Y1 - 2019/11/1
N2 - 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.
AB - 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.
KW - Ciona intestinalis type A (C. robusta)
KW - ascidian
KW - chromosomal inversion
KW - genome
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U2 - 10.1093/gbe/evz228
DO - 10.1093/gbe/evz228
M3 - Article
C2 - 31621849
AN - SCOPUS:85074673806
VL - 11
SP - 3144
EP - 3157
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
SN - 1759-6653
IS - 11
ER -