171
Continuing Evolution of Xenopus Genome
Shapira, E., Marom, K., Yelin, R., Levy, A., Fainsod, A., 1999. A
role for the homeobox gene Xvex-1 as part of the BMP-4
ventral signaling pathway. Mech. Dev. 86, 99–111. https://
doi.org/10.1016/S0925-4773(99)00120-3
Sun, Y.B., Xiong, Z.J., Xiang, X.Y., Liu, S.P., Zhou, W.W., Tu,
X.L., Zhong, L., Wang, L., Wu, D.D., Zhang, B.L., Zhu,
C.L., Yang, M.M., Chen, H.M., Li, F., Zhou, L., Feng, S.H.,
Huang, C., Zhang, G.J., Irwin, D., Hillis, D.M., Murphy,
R.W., Yang, H.M., Che, J., Wang, J., Zhang, Y.P., 2015.
Whole-genome sequence of the Tibetan frog Nanorana
parkeri and the comparative evolution of tetrapod genomes.
Proc. Natl. Acad. Sci. U. S. A. 112, E1257–E1262. https://
doi.org/10.1073/pnas.1501764112
Suzuki, A., Uno, Y., Takahashi, S., Grimwood, J., Schmutz, J.,
Mawaribuchi, S., Yoshida, H., Takebayashi-Suzuki, K., Ito,
M., Matsuda, Y., Rokhsar, D., Taira, M., 2017a. Genome
organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Dev. Biol. 426, 236–244.
https://doi.org/10.1016/j.ydbio.2016.04.014
Suzuki, A., Yoshida, H., van Heeringen, S.J., Takebayashi-Suzuki,
K., Veenstra, G.J.C., Taira, M., 2017b. Genomic organization and modulation of gene expression of the TGF-β and
FGF pathways in the allotetraploid frog Xenopus laevis.
Dev. Biol. 426, 336–359. https://doi.org/10.1016/j.ydbio.
2016.09.016
Suzuki, K.-I.T., Suzuki, M., Shigeta, M., Fortriede, J.D., Takahashi,
S., Mawaribuchi, S., Yamamoto, T., Taira, M., Fukui, A.,
2017. Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis. Dev. Biol. 426, 384–392.
https://doi.org/10.1016/j.ydbio.2016.10.018
Tanaka, T., Ochi, H., Takahashi, S., Ueno, N., Taira, M., 2017.
Genes coding for cyclin-dependent kinase inhibitors are
fragile in Xenopus. Dev. Biol. 426, 291–300. https://doi.
org/10.1016/j.ydbio.2016.06.019
Tinsley, R.C., Loumont, C., Kobel, H.R., 1996. Geographical
distribution and ecology. In: Tinsley, R.C., Kobel, H.R.
(Eds.), The Biology of Xenopus. Clarendon Press, Oxford,
pp. 35–59.
Tour, E., Pillemer, G., Gruenbaum, Y., Fainsod, A., 2001. The
two Xenopus Gbx2 genes exhibit similar, but not identical expression patterns and can affect head formation.
FEBS Lett. 507, 205–209. https://doi.org/10.1016/S00145793(01)02963-5
Uno, Y., Nishida, C., Takagi, C., Ueno, N., Matsuda, Y.,
2013. Homoeologous chromosomes of Xenopus laevis
are highly conserved after whole-genome duplication.
Heredity (Edinb). 111, 430–436. https://doi.org/10.1038/
hdy.2013.65
Watanabe, M., Yasuoka, Y., Mawaribuchi, S., Kuretani, A., Ito,
M., Kondo, M., Ochi, H., Ogino, H., Fukui, A., Taira, M.,
Kinoshita, T., 2017. Conservatism and variability of gene
expression profles among homeologous transcription factors in Xenopus laevis. Dev. Biol. 426, 301–324. https://doi.
org/10.1016/j.ydbio.2016.09.017
Wells, D.E., Gutierrez, L., Xu, Z., Krylov, V., Macha, J.,
Blankenburg, K.P., Hitchens, M., Bellot, L.J., Spivey, M.,
Stemple, D.L., Kowis, A., Ye, Y., Pasternak, S., Owen,
J., Tran, T., Slavikova, R., Tumova, L., Tlapakova, T.,
Seifertova, E., Scherer, S.E., Sater, A.K., 2011. A genetic
map of Xenopus tropicalis. Dev. Biol. 354, 1–8. https://doi.
org/10.1016/j.ydbio.2011.03.022
Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K.,
Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., Talbot, W.S.,
2005. The zebrafsh gene map defnes ancestral vertebrate
chromosomes. Genome Res. 15, 1307–1314. https://doi.
org/10.1101/gr.4134305
Wright, C.V., Cho, K.W., Fritz, A., Bürglin, T.R., De Robertis,
E.M., 1987. A Xenopus laevis gene encodes both homeobox-containing and homeobox-less transcripts. EMBO J. 6,
4083–4094.
Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng,
X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D.,
Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z., Shan, G., Li, X., Wu,
S., Song, Lipu, Hou, G., Jiang, Y., Jeney, Z., Yu, D., Wang, L.,
Shao, C., Song, Lai, Sun, J., Ji, P., Wang, Jian, Li, Q., Xu, L.,
Sun, F., Feng, J., Wang, C., Wang, S., Wang, B., Li, Y., Zhu, Y.,
Xue, W., Zhao, L., Wang, Jintu, Gu, Y., Lv, W., Wu, K., Xiao,
J., Wu, J., Zhang, Z., Yu, J., Sun, X., 2014. Genome sequence
and genetic diversity of the common carp, Cyprinus carpio.
Nat. Genet. 46, 1212–1219. https://doi.org/10.1038/ng.3098
Xu, R.-H., Kim, J., Taira, M., Lin, J.-J., Zhang, C.-H., Sredni, D.,
Evans, T., Kung, H.-F., 1997. Differential regulation of neurogenesis by the two Xenopus GATA-1 genes. Mol. Cell.
Biol. 17, 436–443.
Yager, D.D., 1996. Sound production and acoustic communication
in Xenopus borealis. In: Tinsley, R.C., Kobel, H.R. (Eds.), The
Biology of Xenopus. Clarendon Press, Oxford, pp. 121–141.
Yoshimoto, S., Okada, E., Umemoto, H., Tamura, K., Uno, Y.,
Nishida-Umehara, C., Matsuda, Y., Takamatsu, N., Shiba, T.,
Ito, M., 2008. A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis. Proc.
Natl. Acad. Sci. U.S.A. 105, 2469–2474.
Continuing Evolution of Xenopus Genome
Shapira, E., Marom, K., Yelin, R., Levy, A., Fainsod, A., 1999. A
role for the homeobox gene Xvex-1 as part of the BMP-4
ventral signaling pathway. Mech. Dev. 86, 99–111. https://
doi.org/10.1016/S0925-4773(99)00120-3
Sun, Y.B., Xiong, Z.J., Xiang, X.Y., Liu, S.P., Zhou, W.W., Tu,
X.L., Zhong, L., Wang, L., Wu, D.D., Zhang, B.L., Zhu,
C.L., Yang, M.M., Chen, H.M., Li, F., Zhou, L., Feng, S.H.,
Huang, C., Zhang, G.J., Irwin, D., Hillis, D.M., Murphy,
R.W., Yang, H.M., Che, J., Wang, J., Zhang, Y.P., 2015.
Whole-genome sequence of the Tibetan frog Nanorana
parkeri and the comparative evolution of tetrapod genomes.
Proc. Natl. Acad. Sci. U. S. A. 112, E1257–E1262. https://
doi.org/10.1073/pnas.1501764112
Suzuki, A., Uno, Y., Takahashi, S., Grimwood, J., Schmutz, J.,
Mawaribuchi, S., Yoshida, H., Takebayashi-Suzuki, K., Ito,
M., Matsuda, Y., Rokhsar, D., Taira, M., 2017a. Genome
organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Dev. Biol. 426, 236–244.
https://doi.org/10.1016/j.ydbio.2016.04.014
Suzuki, A., Yoshida, H., van Heeringen, S.J., Takebayashi-Suzuki,
K., Veenstra, G.J.C., Taira, M., 2017b. Genomic organization and modulation of gene expression of the TGF-β and
FGF pathways in the allotetraploid frog Xenopus laevis.
Dev. Biol. 426, 336–359. https://doi.org/10.1016/j.ydbio.
2016.09.016
Suzuki, K.-I.T., Suzuki, M., Shigeta, M., Fortriede, J.D., Takahashi,
S., Mawaribuchi, S., Yamamoto, T., Taira, M., Fukui, A.,
2017. Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis. Dev. Biol. 426, 384–392.
https://doi.org/10.1016/j.ydbio.2016.10.018
Tanaka, T., Ochi, H., Takahashi, S., Ueno, N., Taira, M., 2017.
Genes coding for cyclin-dependent kinase inhibitors are
fragile in Xenopus. Dev. Biol. 426, 291–300. https://doi.
org/10.1016/j.ydbio.2016.06.019
Tinsley, R.C., Loumont, C., Kobel, H.R., 1996. Geographical
distribution and ecology. In: Tinsley, R.C., Kobel, H.R.
(Eds.), The Biology of Xenopus. Clarendon Press, Oxford,
pp. 35–59.
Tour, E., Pillemer, G., Gruenbaum, Y., Fainsod, A., 2001. The
two Xenopus Gbx2 genes exhibit similar, but not identical expression patterns and can affect head formation.
FEBS Lett. 507, 205–209. https://doi.org/10.1016/S00145793(01)02963-5
Uno, Y., Nishida, C., Takagi, C., Ueno, N., Matsuda, Y.,
2013. Homoeologous chromosomes of Xenopus laevis
are highly conserved after whole-genome duplication.
Heredity (Edinb). 111, 430–436. https://doi.org/10.1038/
hdy.2013.65
Watanabe, M., Yasuoka, Y., Mawaribuchi, S., Kuretani, A., Ito,
M., Kondo, M., Ochi, H., Ogino, H., Fukui, A., Taira, M.,
Kinoshita, T., 2017. Conservatism and variability of gene
expression profles among homeologous transcription factors in Xenopus laevis. Dev. Biol. 426, 301–324. https://doi.
org/10.1016/j.ydbio.2016.09.017
Wells, D.E., Gutierrez, L., Xu, Z., Krylov, V., Macha, J.,
Blankenburg, K.P., Hitchens, M., Bellot, L.J., Spivey, M.,
Stemple, D.L., Kowis, A., Ye, Y., Pasternak, S., Owen,
J., Tran, T., Slavikova, R., Tumova, L., Tlapakova, T.,
Seifertova, E., Scherer, S.E., Sater, A.K., 2011. A genetic
map of Xenopus tropicalis. Dev. Biol. 354, 1–8. https://doi.
org/10.1016/j.ydbio.2011.03.022
Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K.,
Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., Talbot, W.S.,
2005. The zebrafsh gene map defnes ancestral vertebrate
chromosomes. Genome Res. 15, 1307–1314. https://doi.
org/10.1101/gr.4134305
Wright, C.V., Cho, K.W., Fritz, A., Bürglin, T.R., De Robertis,
E.M., 1987. A Xenopus laevis gene encodes both homeobox-containing and homeobox-less transcripts. EMBO J. 6,
4083–4094.
Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng,
X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D.,
Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z., Shan, G., Li, X., Wu,
S., Song, Lipu, Hou, G., Jiang, Y., Jeney, Z., Yu, D., Wang, L.,
Shao, C., Song, Lai, Sun, J., Ji, P., Wang, Jian, Li, Q., Xu, L.,
Sun, F., Feng, J., Wang, C., Wang, S., Wang, B., Li, Y., Zhu, Y.,
Xue, W., Zhao, L., Wang, Jintu, Gu, Y., Lv, W., Wu, K., Xiao,
J., Wu, J., Zhang, Z., Yu, J., Sun, X., 2014. Genome sequence
and genetic diversity of the common carp, Cyprinus carpio.
Nat. Genet. 46, 1212–1219. https://doi.org/10.1038/ng.3098
Xu, R.-H., Kim, J., Taira, M., Lin, J.-J., Zhang, C.-H., Sredni, D.,
Evans, T., Kung, H.-F., 1997. Differential regulation of neurogenesis by the two Xenopus GATA-1 genes. Mol. Cell.
Biol. 17, 436–443.
Yager, D.D., 1996. Sound production and acoustic communication
in Xenopus borealis. In: Tinsley, R.C., Kobel, H.R. (Eds.), The
Biology of Xenopus. Clarendon Press, Oxford, pp. 121–141.
Yoshimoto, S., Okada, E., Umemoto, H., Tamura, K., Uno, Y.,
Nishida-Umehara, C., Matsuda, Y., Takamatsu, N., Shiba, T.,
Ito, M., 2008. A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis. Proc.
Natl. Acad. Sci. U.S.A. 105, 2469–2474.