170
Xenopus
development in the medaka f sh. Nature 417, 559–563. https://
doi.org/10.1038/nature751
Matsuda, Y., Uno, Y., Kondo, M., Gilchrist, M.J., Zorn, A.M.,
Rokhsar, D.S., Schmid, M., Taira, M., 2015. A new
nomenclature of Xenopus laevis chromosomes based on the
phylogenetic relationship to silurana/Xenopus tropicalis. Cytogenet. Genome Res. 145, 187–191. https://doi.org/10.1159/
000381292
Mawaribuchi, S., Takahashi, S., Wada, M., Uno, Y., Matsuda,
Y., Kondo, M., Fukui, A., Takamatsu, N., Taira, M., Ito,
M., 2017. Sex chromosome differentiation and the W- and
Z-specifc loci in Xenopus laevis. Dev. Biol. 426, 393–400.
https://doi.org/10.1016/j.ydbio.2016.06.015
McClintock, B., 1984. The signifcance of responses of the genome
to challenge. Science 226, 792–801. https://doi.org/10.1126/
science.15739260
McStay, B., 2006. Nucleolar dominance: A model for rRNA gene
silencing. Genes Dev. 20, 1207–1214. https://doi.org/10.1101/
gad.1436906
Meyer, A., Van de Peer, Y., 2005. From 2R to 3R: Evidence for
a f sh-specifc genome duplication (FSGD). BioEssays 27,
937–945. https://doi.org/10.1002/bies.20293
Michalak, K., Maciak, S., Kim, Y.B., Santopietro, G., Oh, J.H.,
Kang, L., Garner, H.R., Michalak, P., 2015. Nucleolar dominance and maternal control of 45S rDNA expression. Proc.
R. Soc. B Biol. Sci. 282, 20152201. https://doi.org/10.1098/
rspb.2015.2201
Michiue, T., Yamamoto, T., Yasuoka, Y., Goto, T., Ikeda, T., Nagura,
K., Nakayama, T., Taira, M., Kinoshita, T., 2017. High variability of expression profles of homeologous genes for
Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus
laevis. Dev. Biol. 426, 270–290. https://doi.org/10.1016/j.
ydbio.2016.12.006
Mouse Genome Sequencing Consortium, 2002. Initial sequencing and comparative analysis of the mouse genome. Nature
420, 520–562.
Müller, M.M., Carrasco, A.E., De Robertis, E.M., 1984. A
homeo-box-containing gene expressed during oogenesis in
Xenopus. Cell 39, 157–162. https://doi.org/10.1016/00928674(84)90201-0
Müller, W.P., 1977. Diplotene chromosomes of Xenopus hybrid
oocytes. Chromosom 59, 273–282.
Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo,
D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert,
K.H.J., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou,
H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley,
E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z., Liang,
Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X., Rubin,
G.M., Adams, M.D., Venter, J.C., 2000. A whole-genome
assembly of Drosophila. Science 287, 2196–2204. https://
doi.org/10.1126/science.287.5461.2196
Nakayama, T., Nakajima, K., Cox, A., Fisher, M., Howell, M., Fish,
M.B., Yaoita, Y., Grainger, R.M., 2017. No privacy, a Xenopus
tropicalis mutant, is a model of human Hermansky-Pudlak
syndrome and allows visualization of internal organogenesis during tadpole development. Dev. Biol. 426, 472−486.
https://doi.org/10.1016/j.ydbio.2016.08.020
Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C.,
Shimizu, A., Shan, Z., Haaf, T., Shimizu, N., Shima, A.,
Schmid, M., Schartl, M., 2002. A duplicated copy of
DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc. Natl. Acad. Sci.
U. S. A. 99, 11778–11783. https://doi.org/10.1073/pnas.
182314699
Owens, N.D.L., Blitz, I.L., Maura, A., Gilchrist, M.J., Ken, W.Y.,
Khokha, M.K., Owens, N.D.L., Blitz, I.L., Lane, M.A.,
Patrushev, I., Overton, J.D., Gilchrist, M.J., 2016. Measuring
absolute RNA copy numbers at high temporal resolution
reveals transcriptome kinetics in development. Cell Rep. 14,
632–647. https://doi.org/10.1016/j.celrep.2015.12.050
Pascual-Anaya, J., D’Aniello, S., Kuratani, S., Garcia-Fernàndez,
J., 2013. Evolution of hox gene clusters in deuterostomes.
BMC Dev. Biol. 13, 26. https://doi.org/10.1186/1471-213X13-26
Picker, M.D., Harrison, J.A., Wallace, D., 1996. Natural hybridization between Xenopus laevis laevis and X. gilli in the
south-western Cape Province, South Africa. In: Tinsley,
R.C., Kobel, H.R. (Eds.), The Biology of Xenopus. Clarendon
Press, Oxford, pp. 61–71.
Poczai, P., Cernák, I., Varga, I., Hyvönen, J., 2014. Analysis of the
genome sequence of the fowering plant Arabidopsis thaliana. Genet. Resour. Crop Evol. 61, 796–815. https://doi.
org/10.1134/S1022795411020074
Preuss, S., Pikaard, C.S., 2007. rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch. Biochim. Biophys. Acta: Gene Struct.
Expr. 1769, 383–392.https://doi.org/10.1016/j.bbaexp.2007.
02.005
Putnam, N.H., O’Connell, B.L., Stites, J.C., Rice, B.J., Blanchette,
M., Calef, R., Troll, C.J., Fields, A., Hartley, P.D., Sugnet, C.W.,
Haussler, D., Rokhsar, D.S., Green, R.E., 2016. Chromosomescale shotgun assembly using an in vitro method for longrange linkage. Genome Res 26, 342–350. https://doi.org/
10.1101/gr.193474.115
Rebagliati, M.R., Weeks, D.L., Harvey, R.P., Melton, D.A., 1985.
Identifcation and cloning of localized maternal RNAs from
Xenopus eggs. Cell 42, 769–777. https://doi.org/https://doi.
org/10.1016/0092-8674(85)90273-9
Reinschmidt, D.C., Simon, S.J., Volpe, E.P., Tompkins, R., 1979.
Production of tetraploid and homozygous diploid amphibians by suppression of frst cleavage. J. Exp. Zool. 210, 137–
143. https://doi.org/10.1002/jez.1402100115
Robert, J., Ohta, Y., 2009. Comparative and developmental study of
the immune system in Xenopus. Dev. Dyn. 238, 1249–1270.
https://doi.org/10.1002/dvdy.21891
Schmid, M., Steinlein, C., 1991. Chromosome banding in AmphibiaXVI: High-resolution replication banding patterns in Xenopus
laevis. Chromosoma 101, 123–132. https://doi.org/10.1007/
BF00357062
Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A.,
Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo,
M., Van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H.,
Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam,
N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe,
M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe,
S.S., Van Kruijsbergen, I., Shu, S., Carlson, J., Kinoshita,
T., Ohta, Y., Mawaribuchi, S., Jenkins, J., Grimwood,
J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y.,
Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller,
K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu,
Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi,
K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston,
D.W., Shendure, J., Dupasquier, L., Vize, P.D., Zorn, A.M.,
Ito, M., Marcotte, E.M., Wallingford, J.B., Ito, Y., Asashima,
M., Ueno, N., Matsuda, Y., Veenstra, G.J.C., Fujiyama, A.,
Harland, R.M., Taira, M., Rokhsar, D.S., 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538,
336–343. https://doi.org/10.1038/nature19840
Xenopus
development in the medaka f sh. Nature 417, 559–563. https://
doi.org/10.1038/nature751
Matsuda, Y., Uno, Y., Kondo, M., Gilchrist, M.J., Zorn, A.M.,
Rokhsar, D.S., Schmid, M., Taira, M., 2015. A new
nomenclature of Xenopus laevis chromosomes based on the
phylogenetic relationship to silurana/Xenopus tropicalis. Cytogenet. Genome Res. 145, 187–191. https://doi.org/10.1159/
000381292
Mawaribuchi, S., Takahashi, S., Wada, M., Uno, Y., Matsuda,
Y., Kondo, M., Fukui, A., Takamatsu, N., Taira, M., Ito,
M., 2017. Sex chromosome differentiation and the W- and
Z-specifc loci in Xenopus laevis. Dev. Biol. 426, 393–400.
https://doi.org/10.1016/j.ydbio.2016.06.015
McClintock, B., 1984. The signifcance of responses of the genome
to challenge. Science 226, 792–801. https://doi.org/10.1126/
science.15739260
McStay, B., 2006. Nucleolar dominance: A model for rRNA gene
silencing. Genes Dev. 20, 1207–1214. https://doi.org/10.1101/
gad.1436906
Meyer, A., Van de Peer, Y., 2005. From 2R to 3R: Evidence for
a f sh-specifc genome duplication (FSGD). BioEssays 27,
937–945. https://doi.org/10.1002/bies.20293
Michalak, K., Maciak, S., Kim, Y.B., Santopietro, G., Oh, J.H.,
Kang, L., Garner, H.R., Michalak, P., 2015. Nucleolar dominance and maternal control of 45S rDNA expression. Proc.
R. Soc. B Biol. Sci. 282, 20152201. https://doi.org/10.1098/
rspb.2015.2201
Michiue, T., Yamamoto, T., Yasuoka, Y., Goto, T., Ikeda, T., Nagura,
K., Nakayama, T., Taira, M., Kinoshita, T., 2017. High variability of expression profles of homeologous genes for
Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus
laevis. Dev. Biol. 426, 270–290. https://doi.org/10.1016/j.
ydbio.2016.12.006
Mouse Genome Sequencing Consortium, 2002. Initial sequencing and comparative analysis of the mouse genome. Nature
420, 520–562.
Müller, M.M., Carrasco, A.E., De Robertis, E.M., 1984. A
homeo-box-containing gene expressed during oogenesis in
Xenopus. Cell 39, 157–162. https://doi.org/10.1016/00928674(84)90201-0
Müller, W.P., 1977. Diplotene chromosomes of Xenopus hybrid
oocytes. Chromosom 59, 273–282.
Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo,
D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert,
K.H.J., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou,
H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley,
E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z., Liang,
Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X., Rubin,
G.M., Adams, M.D., Venter, J.C., 2000. A whole-genome
assembly of Drosophila. Science 287, 2196–2204. https://
doi.org/10.1126/science.287.5461.2196
Nakayama, T., Nakajima, K., Cox, A., Fisher, M., Howell, M., Fish,
M.B., Yaoita, Y., Grainger, R.M., 2017. No privacy, a Xenopus
tropicalis mutant, is a model of human Hermansky-Pudlak
syndrome and allows visualization of internal organogenesis during tadpole development. Dev. Biol. 426, 472−486.
https://doi.org/10.1016/j.ydbio.2016.08.020
Nanda, I., Kondo, M., Hornung, U., Asakawa, S., Winkler, C.,
Shimizu, A., Shan, Z., Haaf, T., Shimizu, N., Shima, A.,
Schmid, M., Schartl, M., 2002. A duplicated copy of
DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc. Natl. Acad. Sci.
U. S. A. 99, 11778–11783. https://doi.org/10.1073/pnas.
182314699
Owens, N.D.L., Blitz, I.L., Maura, A., Gilchrist, M.J., Ken, W.Y.,
Khokha, M.K., Owens, N.D.L., Blitz, I.L., Lane, M.A.,
Patrushev, I., Overton, J.D., Gilchrist, M.J., 2016. Measuring
absolute RNA copy numbers at high temporal resolution
reveals transcriptome kinetics in development. Cell Rep. 14,
632–647. https://doi.org/10.1016/j.celrep.2015.12.050
Pascual-Anaya, J., D’Aniello, S., Kuratani, S., Garcia-Fernàndez,
J., 2013. Evolution of hox gene clusters in deuterostomes.
BMC Dev. Biol. 13, 26. https://doi.org/10.1186/1471-213X13-26
Picker, M.D., Harrison, J.A., Wallace, D., 1996. Natural hybridization between Xenopus laevis laevis and X. gilli in the
south-western Cape Province, South Africa. In: Tinsley,
R.C., Kobel, H.R. (Eds.), The Biology of Xenopus. Clarendon
Press, Oxford, pp. 61–71.
Poczai, P., Cernák, I., Varga, I., Hyvönen, J., 2014. Analysis of the
genome sequence of the fowering plant Arabidopsis thaliana. Genet. Resour. Crop Evol. 61, 796–815. https://doi.
org/10.1134/S1022795411020074
Preuss, S., Pikaard, C.S., 2007. rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch. Biochim. Biophys. Acta: Gene Struct.
Expr. 1769, 383–392.https://doi.org/10.1016/j.bbaexp.2007.
02.005
Putnam, N.H., O’Connell, B.L., Stites, J.C., Rice, B.J., Blanchette,
M., Calef, R., Troll, C.J., Fields, A., Hartley, P.D., Sugnet, C.W.,
Haussler, D., Rokhsar, D.S., Green, R.E., 2016. Chromosomescale shotgun assembly using an in vitro method for longrange linkage. Genome Res 26, 342–350. https://doi.org/
10.1101/gr.193474.115
Rebagliati, M.R., Weeks, D.L., Harvey, R.P., Melton, D.A., 1985.
Identifcation and cloning of localized maternal RNAs from
Xenopus eggs. Cell 42, 769–777. https://doi.org/https://doi.
org/10.1016/0092-8674(85)90273-9
Reinschmidt, D.C., Simon, S.J., Volpe, E.P., Tompkins, R., 1979.
Production of tetraploid and homozygous diploid amphibians by suppression of frst cleavage. J. Exp. Zool. 210, 137–
143. https://doi.org/10.1002/jez.1402100115
Robert, J., Ohta, Y., 2009. Comparative and developmental study of
the immune system in Xenopus. Dev. Dyn. 238, 1249–1270.
https://doi.org/10.1002/dvdy.21891
Schmid, M., Steinlein, C., 1991. Chromosome banding in AmphibiaXVI: High-resolution replication banding patterns in Xenopus
laevis. Chromosoma 101, 123–132. https://doi.org/10.1007/
BF00357062
Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A.,
Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo,
M., Van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H.,
Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam,
N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe,
M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe,
S.S., Van Kruijsbergen, I., Shu, S., Carlson, J., Kinoshita,
T., Ohta, Y., Mawaribuchi, S., Jenkins, J., Grimwood,
J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y.,
Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller,
K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu,
Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi,
K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston,
D.W., Shendure, J., Dupasquier, L., Vize, P.D., Zorn, A.M.,
Ito, M., Marcotte, E.M., Wallingford, J.B., Ito, Y., Asashima,
M., Ueno, N., Matsuda, Y., Veenstra, G.J.C., Fujiyama, A.,
Harland, R.M., Taira, M., Rokhsar, D.S., 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538,
336–343. https://doi.org/10.1038/nature19840