169
Continuing Evolution of Xenopus Genome
laevis and Xenopus mulleri. J. Mol. Biol. 80, 217–228. https://
doi.org/10.1016/0022-2836(73)90168-X
Hori, Y., Shimamoto, A., Kobayashi, T., 2021. The human ribosomal DNA array is composed of highly homogenized tandem clusters. Genome Res August, gr.275838.121. https://doi.
org/10.1101/gr.275838.121
Igawa, T., Watanabe, A., Suzuki, A., Kashiwagi, A., Kashiwagi, K.,
Noble, A., Guille, M., Simpson, D.E., Horb, M.E., Fujii, T.,
Sumida, M., 2015. Inbreeding ratio and genetic relationships
among strains of the western clawed frog, Xenopus tropicalis. PLoS One 10, e0133963. https://doi.org/10.1371/journal.
pone.0133963
Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, K., Nishida, M., 2015.
Rapid genome reshaping by multiple-gene loss after wholegenome duplication in teleost fsh suggested by mathematical
modeling. Proc. Natl. Acad. Sci. 112, 14918–14923. https://
doi.org/10.1073/pnas.1507669112
International Chicken Genome Sequencing Consortium, 2004.
Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution. Nature
432, 695–716. https://doi.org/10.1038/nature03154
International Human Genome Sequencing Consortium, 2001. Initial
sequencing and analysis of the human genome. Nature 409,
860–921.
Izutsu, Y., Yoshizato, K., 1993. Metamorphosis-dependent recognition of larval skin as non-self by inbred adult frogs ( Xenopus
laevis). J. Exp. Zool. 266, 163–167. https://doi.org/10.1002/
jez.1402660211
Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan,
B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo,
T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y.,
Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu,
N., Hashimoto, S.I., Yang, J., Lee, Y., Matsushima, K.,
Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S.,
Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T.,
Shin-I, T., Takeda, H., Morishita, S., Kohara, Y., 2007. The
medaka draft genome and insights into vertebrate genome
evolution. Nature 447, 714–719. https://doi.org/10.1038/
nature05846
Kawahara, H., 1978. Production of triploid and gynogenetic diploid Xenopus by cold treatment. Dev. Growth Differ. 20,
227–236. https://doi.org/10.1111/j.1440-169X.1978.00227.x
Kawamura, T., Nishioka, M., 1983. Reproductive capacity of
male autotetraploid Rana nigromaculata and male and
female amphidiploids produced from them by mating with
female diploid Rana brevipoda. Sci. Rep. Lab. Amphib. Biol.
Hiroshima Univ. 6, 1–45.
Kawamura, T., Nishioka, M., 1960. Amphidiploid frogs produced
by artifcial means. J. Sci. Hiroshima Univ., Ser. B. Div. I 18,
195–220.
Khokha, M.K., Krylov, V., Reilly, M.J., Gall, J.G., Bhattacharya,
D., Cheung, C.Y.J., Kaufman, S., Dang, K.L., Macha, J.,
Ngo, C., Prakash, N., Schmidt, P., Tlapakova, T., Trivedi, T.,
Tumova, L., Abu-Daya, A., Geach, T., Vendrell, E., Ironf eld,
H., Sinzelle, L., Sater, A.K., Wells, D.E., Harland, R.M.,
Zimmerman, L.B., 2009. Rapid gynogenetic mapping of
Xenopus tropicalis mutations to chromosomes. Dev. Dyn.
238, 1398–1406. https://doi.org/10.1002/dvdy.21965
Kobel, H.R., 1996. Allopolyploid speciation. In: Tinsley, R.C.,
Kobel, H.R. (Eds.), The Biology of Xenopus. Clarendon Press,
Oxford, pp. 391–401.
Kobel, H.R., 1981. Evolutionary trends in Xenopus (Anura
Pipidae). Monit. Zool. Ital. Suppl. 15, 119–131. https://doi.
org/10.1080/03749444.1981.10736632
Kobel, H.R., Du Pasquier, L., 1986. Genetics of polyploid
Xenopus. Trends Genet. 2, 310–315. https://doi.org/10.1016/
0168-9525(86)90286-6
Kobel, H.R., Du Pasquier, L., 1975. Production of large clones
of histocompatible, fully identical clawed toads (Xenopus).
Immunogenetics 2, 87–91.
Kobel, H.R., Du Pasquier, L., Tinsley, R.C., 1981. Natural hybridization and gene introgression between Xenopus gilli and
Xenopus laevis laevis (Anura: Pipidae). J. Zool. 194, 317–322.
https://doi.org/10.1111/j.1469-7998.1981.tb04584.x
Kondo, M., Matsuo, M., Igarashi, K., Haramoto, Y., Yamamoto,
T., Yasuoka, Y., Taira, M., 2019. De novo transcription of
multiple Hox cluster genes takes place simultaneously in
early Xenopus tropicalis embryos. Biol. Open 8, bio038422.
https://doi.org/10.1242/bio.038422
Kondo, M., Nanda, I., Hornung, U., Asakawa, S., Shimizu, N.,
Mitani, H., Schmid, M., Shima, A., Schartl, M., 2003.
Absence of the candidate male sex-determining gene dmrt1b(Y) of medaka from other fsh species. Curr. Biol. 13, 416–
420. https://doi.org/10.1016/s0960-9822(03)00125-8
Kondo, M., Nanda, I., Hornung, U., Schmid, M., Schartl, M., 2004.
Evolutionary origin of the medaka Y chromosome. Curr.
Biol. 14, 1664–1669. https://doi.org/10.1016/j
Kondo, M., Yamamoto, T., Takahashi, S., Taira, M., 2017. Comprehensive analyses of hox gene expression in Xenopus laevis
embryos and adult tissues. Dev. Growth Differ. 59, 526–539.
https://doi.org/10.1111/dgd.12382
Kuraku, S., Meyer, A., 2009. The evolution and maintenance of
Hox gene clusters in vertebrates and the teleost-specif c
genome duplication. Int. J. Dev. Biol. 53, 765–773. https://
doi.org/10.1387/ijdb.072533km
Laurent, M.N., Blitz, I.L., Hashimoto, C., Rothbächer, U., Cho,
K.W.Y., 1997. The Xenopus homeobox gene Twin mediates
Wnt induction of Goosecoid in establishment of Spemann’s
organizer. Development 124, 4905–4916.
Lieberman-Aiden, E., Van Berkum, N.L., Williams, L., Imakaev,
M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo,
P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender,
M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J.,
Mirny, L.A., Lander, E.S., Dekker, J., 2009. Comprehensive
mapping of long-range interactions reveals folding principles
of the human genome. Science 326, 289–293. https://doi.
org/10.1126/science.1181369
Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome,
T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin,
A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B.,
Hermansen, R.A., Von Schalburg, K., Rondeau, E.B., Di
Genova, A., Samy, J.K.A., Olav Vik, J., Vigeland, M.D.,
Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., De Jong,
P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A.,
Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S.,
Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra,
P., Jones, S.J.M., Jonassen, I., Maass, A., Omholt, S.W.,
Davidson, W.S., 2016. The Atlantic salmon genome provides
insights into rediploidization. Nature 533, 200–205. https://
doi.org/10.1038/nature17164
Malone, J.H., Chrzanowski, T.H., Michalak, P., 2007. Sterility and
gene expression in hybrid males of Xenopus laevis and X.
muelleri. PLoS One 2, e781. https://doi.org/10.1371/journal.
pone.0000781
Matsuda, M., Nagahama, Y., Shinomiya, A., Sato, T., Matsuda,
C., Kobayashi, T., Morrey, C.E., Shibata, N., Asakawa, S.,
Shimizu, N., Hori, H., Hamaguchi, S., Sakaizumi, M., 2002.
DMY is a Y-specifc DM-domain gene required for male
Continuing Evolution of Xenopus Genome
laevis and Xenopus mulleri. J. Mol. Biol. 80, 217–228. https://
doi.org/10.1016/0022-2836(73)90168-X
Hori, Y., Shimamoto, A., Kobayashi, T., 2021. The human ribosomal DNA array is composed of highly homogenized tandem clusters. Genome Res August, gr.275838.121. https://doi.
org/10.1101/gr.275838.121
Igawa, T., Watanabe, A., Suzuki, A., Kashiwagi, A., Kashiwagi, K.,
Noble, A., Guille, M., Simpson, D.E., Horb, M.E., Fujii, T.,
Sumida, M., 2015. Inbreeding ratio and genetic relationships
among strains of the western clawed frog, Xenopus tropicalis. PLoS One 10, e0133963. https://doi.org/10.1371/journal.
pone.0133963
Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, K., Nishida, M., 2015.
Rapid genome reshaping by multiple-gene loss after wholegenome duplication in teleost fsh suggested by mathematical
modeling. Proc. Natl. Acad. Sci. 112, 14918–14923. https://
doi.org/10.1073/pnas.1507669112
International Chicken Genome Sequencing Consortium, 2004.
Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution. Nature
432, 695–716. https://doi.org/10.1038/nature03154
International Human Genome Sequencing Consortium, 2001. Initial
sequencing and analysis of the human genome. Nature 409,
860–921.
Izutsu, Y., Yoshizato, K., 1993. Metamorphosis-dependent recognition of larval skin as non-self by inbred adult frogs ( Xenopus
laevis). J. Exp. Zool. 266, 163–167. https://doi.org/10.1002/
jez.1402660211
Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan,
B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo,
T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y.,
Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu,
N., Hashimoto, S.I., Yang, J., Lee, Y., Matsushima, K.,
Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S.,
Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T.,
Shin-I, T., Takeda, H., Morishita, S., Kohara, Y., 2007. The
medaka draft genome and insights into vertebrate genome
evolution. Nature 447, 714–719. https://doi.org/10.1038/
nature05846
Kawahara, H., 1978. Production of triploid and gynogenetic diploid Xenopus by cold treatment. Dev. Growth Differ. 20,
227–236. https://doi.org/10.1111/j.1440-169X.1978.00227.x
Kawamura, T., Nishioka, M., 1983. Reproductive capacity of
male autotetraploid Rana nigromaculata and male and
female amphidiploids produced from them by mating with
female diploid Rana brevipoda. Sci. Rep. Lab. Amphib. Biol.
Hiroshima Univ. 6, 1–45.
Kawamura, T., Nishioka, M., 1960. Amphidiploid frogs produced
by artifcial means. J. Sci. Hiroshima Univ., Ser. B. Div. I 18,
195–220.
Khokha, M.K., Krylov, V., Reilly, M.J., Gall, J.G., Bhattacharya,
D., Cheung, C.Y.J., Kaufman, S., Dang, K.L., Macha, J.,
Ngo, C., Prakash, N., Schmidt, P., Tlapakova, T., Trivedi, T.,
Tumova, L., Abu-Daya, A., Geach, T., Vendrell, E., Ironf eld,
H., Sinzelle, L., Sater, A.K., Wells, D.E., Harland, R.M.,
Zimmerman, L.B., 2009. Rapid gynogenetic mapping of
Xenopus tropicalis mutations to chromosomes. Dev. Dyn.
238, 1398–1406. https://doi.org/10.1002/dvdy.21965
Kobel, H.R., 1996. Allopolyploid speciation. In: Tinsley, R.C.,
Kobel, H.R. (Eds.), The Biology of Xenopus. Clarendon Press,
Oxford, pp. 391–401.
Kobel, H.R., 1981. Evolutionary trends in Xenopus (Anura
Pipidae). Monit. Zool. Ital. Suppl. 15, 119–131. https://doi.
org/10.1080/03749444.1981.10736632
Kobel, H.R., Du Pasquier, L., 1986. Genetics of polyploid
Xenopus. Trends Genet. 2, 310–315. https://doi.org/10.1016/
0168-9525(86)90286-6
Kobel, H.R., Du Pasquier, L., 1975. Production of large clones
of histocompatible, fully identical clawed toads (Xenopus).
Immunogenetics 2, 87–91.
Kobel, H.R., Du Pasquier, L., Tinsley, R.C., 1981. Natural hybridization and gene introgression between Xenopus gilli and
Xenopus laevis laevis (Anura: Pipidae). J. Zool. 194, 317–322.
https://doi.org/10.1111/j.1469-7998.1981.tb04584.x
Kondo, M., Matsuo, M., Igarashi, K., Haramoto, Y., Yamamoto,
T., Yasuoka, Y., Taira, M., 2019. De novo transcription of
multiple Hox cluster genes takes place simultaneously in
early Xenopus tropicalis embryos. Biol. Open 8, bio038422.
https://doi.org/10.1242/bio.038422
Kondo, M., Nanda, I., Hornung, U., Asakawa, S., Shimizu, N.,
Mitani, H., Schmid, M., Shima, A., Schartl, M., 2003.
Absence of the candidate male sex-determining gene dmrt1b(Y) of medaka from other fsh species. Curr. Biol. 13, 416–
420. https://doi.org/10.1016/s0960-9822(03)00125-8
Kondo, M., Nanda, I., Hornung, U., Schmid, M., Schartl, M., 2004.
Evolutionary origin of the medaka Y chromosome. Curr.
Biol. 14, 1664–1669. https://doi.org/10.1016/j
Kondo, M., Yamamoto, T., Takahashi, S., Taira, M., 2017. Comprehensive analyses of hox gene expression in Xenopus laevis
embryos and adult tissues. Dev. Growth Differ. 59, 526–539.
https://doi.org/10.1111/dgd.12382
Kuraku, S., Meyer, A., 2009. The evolution and maintenance of
Hox gene clusters in vertebrates and the teleost-specif c
genome duplication. Int. J. Dev. Biol. 53, 765–773. https://
doi.org/10.1387/ijdb.072533km
Laurent, M.N., Blitz, I.L., Hashimoto, C., Rothbächer, U., Cho,
K.W.Y., 1997. The Xenopus homeobox gene Twin mediates
Wnt induction of Goosecoid in establishment of Spemann’s
organizer. Development 124, 4905–4916.
Lieberman-Aiden, E., Van Berkum, N.L., Williams, L., Imakaev,
M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo,
P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender,
M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J.,
Mirny, L.A., Lander, E.S., Dekker, J., 2009. Comprehensive
mapping of long-range interactions reveals folding principles
of the human genome. Science 326, 289–293. https://doi.
org/10.1126/science.1181369
Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome,
T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin,
A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B.,
Hermansen, R.A., Von Schalburg, K., Rondeau, E.B., Di
Genova, A., Samy, J.K.A., Olav Vik, J., Vigeland, M.D.,
Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., De Jong,
P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A.,
Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S.,
Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra,
P., Jones, S.J.M., Jonassen, I., Maass, A., Omholt, S.W.,
Davidson, W.S., 2016. The Atlantic salmon genome provides
insights into rediploidization. Nature 533, 200–205. https://
doi.org/10.1038/nature17164
Malone, J.H., Chrzanowski, T.H., Michalak, P., 2007. Sterility and
gene expression in hybrid males of Xenopus laevis and X.
muelleri. PLoS One 2, e781. https://doi.org/10.1371/journal.
pone.0000781
Matsuda, M., Nagahama, Y., Shinomiya, A., Sato, T., Matsuda,
C., Kobayashi, T., Morrey, C.E., Shibata, N., Asakawa, S.,
Shimizu, N., Hori, H., Hamaguchi, S., Sakaizumi, M., 2002.
DMY is a Y-specifc DM-domain gene required for male