RT Journal Article
T1 The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians
A1 Kimura, Yuki
A1 Suzuki, Miyuki
A1 Okumura, Akinori
A1 Matsunami, Masatoshi
A1 Nishide, Hiroyo
A1 Mizuno, Rima
A1 Bou, Kazuto
A1 Uno, Yoshinobu
A1 Nakada, Tomoaki
A1 Hasunuma, Itaru
A1 Haramoto, Yoshikazu
A1 Fukui, Akimasa
A1 Inoue, Takeshi
A1 Sato, Yuki
A1 Yamaguchi, Katsushi
A1 Zhang, Zicong
A1 Chihara, Akane
A1 Takehara, Mai
A1 Shibata, Yuki
A1 Kitada, Masaaki
A1 Moreno García, Nerea
A1 Uchiyama, Ikuo
A1 Suzuki, Yutaka
A1 Takeuchi, Takashi
A1 Nikaido, Masato
A1 Agata, Kiyokazu
A1 Toyoda, Atsushi
A1 Shigenobu, Shuji
A1 Hayashi, Toshinori
A1 Suzuki, Ken-ichi T.
AB Salamanders provide excellent models for studying vertebrate evolution, development, and regeneration. To further advance the newt as a model organism in biology, we conducted draft genome sequencing of 20 Gb of an inbred newt (Pleurodeles waltl). As part of this study, the Hoxd11–d13 intergenic region is expanded by over 1 Mb owing to the massive insertion of repetitive sequences including newt-specific satellite DNA. Interestingly, Myod and Bmp4, genes that are typically involved in vertebrate development, are absent in salamanders. Co-option of Sodefrin Precursor-like Factor genes, which encode sex pheromone ligands, suggests a diversification of reproductive behavior among salamanders. Moreover, a limb enhancer of Shh, MFCS1/ZRS, retains its function, even though it is positioned approximately 5 Mb away from the promoter. Furthermore, we have identified a functional cis-element potentially associated with limb regeneration in this enhancer. The newt genome yields crucial insights into amphibian evolution, behavior, development, and regeneration.
PB Cell Press Elsevier
SN 2589-0042
YR 2025
FD 2025-10-17
LK https://hdl.handle.net/20.500.14352/129888
UL https://hdl.handle.net/20.500.14352/129888
LA eng
NO Kimura, Y., Suzuki, M., Okumura, A., Matsunami, M., Nishide, H., Mizuno, R., Bou, K., Uno, Y., Nakada, T., Hasunuma, I., Haramoto, Y., Fukui, A., Inoue, T., Sato, Y., Yamaguchi, K., Zhang, Z., Chihara, A., Takehara, M., Shibata, Y., et al. (2025). The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians. iScience, 28(10). https://doi.org/10.1016/J.ISCI.2025.113535
NO This research was supported by the following funding sources: JST, CREST Grant Number JPMJCR2025 (K.T.S.); JSPS KAKENHI Grant Number JP16H06279 (PAGS); JP21H03829, JP22H04925 (PAGS); JP18K06257, JP22K06822, JP16H04794, JP19K07268, JP22H02796, JP21K20667 (K.T.S., M.T., T.T, T.H., and Y. Shibata); NIBB Collaborative Research Program (22NIBB451, 23NIBB438, 24NIBB457, 25NIBB402, 21NIBB101, 22NIBB201, 23NIBB201) to M.M. and T.H.; and Joint Research of the Exploratory Research Center on Life and Living Systems Grant Numbers 23-S6, 22-S3 (K.T.S).
DS Docta Complutense
RD 26 feb 2026