The Continuing Evolution of
10 the Xenopus Genome
Mariko Kondo and Masanori Taira
CONTENTS
10.1. Genome History of the Genus Xenopus................................................................................................................... 155
10.1.1. Heterosis ................................................................................................................................................... 156
10.1.2. Recognition of Allotetraploidy ................................................................................................................. 156
10.2. Genome Sequencing of Xenopus—The Highlights ................................................................................................. 157
10.2.1. Genome Sequencing of X. tropicalis ........................................................................................................ 157
10.2.2. Sequencing and Assembly of the X. laevis Genome................................................................................. 157
10.2.3. Comparison between X. tropicalis and X. laevis Genomes and Chromosomes........................................ 158
10.2.4. The Real Story of the Identifcation of L and S Subgenomes and Chromosomes .................................... 158
10.2.5. Asymmetrical Evolution of the L and S Subgenomes .............................................................................. 159
10.3. Studies Utilizing the Genome Sequences of Xenopus ............................................................................................. 161
10.3.1. W- and Z-Specifc Re gions in the Sex Chromosomes .............................................................................. 161
10.3.2. Analyses of Hox Genes............................................................................................................................. 162
10.3.3. Detailed Gene Organization in the Xenopus laevis Subgenomes ............................................................. 163
10.4. Conclusions.............................................................................................................................................................. 165
10.5. Future Directions ..................................................................................................................................................... 166
10.5.1. Comparative Genome Analysis ................................................................................................................. 166
10.5.2. Artif cial Hybrid Analysis ......................................................................................................................... 166
10.5.3. Artif cial Allopolyploid Analysis .............................................................................................................. 166
Acknowledgments ................................................................................................................................................................ 167
References............................................................................................................................................................................ 167
Clawed frogs of the genus Xenopus inhabit a large area of
Africa, where 29 extant species are currently recognized (as
of May 2021, https://amphibiaweb.org). Of them, the African
clawed frog Xenopus laevis was originally imported into
Europe from its native South Africa and has been used for
research in laboratories since the 1930s, initially mainly for
endocrinology studies and subsequently for developmental
biology research (reviewed in Gurdon and Hopwood, 2000),
and used as a model system to study cell cycle, oogenesis,
early development, and so on, by biochemical and molecular
biological approaches. X. laevis has various advantages as
a model animal, such as easy rearing and breeding, a wide
range of survival temperatures, resistance to infectious disease, and many others, which might be due to its allotetraploidy. However, from the late 1990s, when developmental in Kobel and Du Pasquier, 1986; Evans et al., 2004; Evans,
genetics started to dominate the feld of developmental
biology using knockout mice and mutagenesis screening
of zebrafsh, the allotetraploidy of X. laevis became a diswith a diploid Xenopus species, X. tropicalis, which has a
simpler genome and shorter generation time. X. tropicalis
was previously called Silurana tropicalis, but later Silurana
was treated as a subgenus; thus, this species was renamed
advantage. Therefore, scientists tried to replace X. laevis a single ancestral species is called autopolyploidy, whereas
Xenopus Silurana tropicalis, commonly called Xenopus
tropicalis. The genus Xenopus now consists of two subgenera, Xenopus and Silurana. Although X. tropicalis is a
suitable diploid model system in amphibians, X. laevis still
remains useful, and hence both X. tropicalis and X. laevis
have continued being used for research.
10.1. GENOME HISTORY OF THE
GENUS XENOPUS
The evolutionary history of Xenopus frogs leading to the
current phylogenetic relationships consist of bifurcating speciation and allopolyploidization by interspecies hybridization followed by polyploidization (Figure 10.1A) (reviewed
2008). Polyploidization is caused by duplication of the entire
genome, otherwise called whole genome duplication (WGD).
Polyploidy originating from duplication of a genome from
allopolyploidy refers to genome duplication of hybrid
genomes via interspecifc crossing, which is the case for
Xenopus species. Allotetraploid genomes, therefore, contain
two different genomes derived from diploid ancestor species,
DOI: 10.1201/9781003050230-12
155
10 the Xenopus Genome
Mariko Kondo and Masanori Taira
CONTENTS
10.1. Genome History of the Genus Xenopus................................................................................................................... 155
10.1.1. Heterosis ................................................................................................................................................... 156
10.1.2. Recognition of Allotetraploidy ................................................................................................................. 156
10.2. Genome Sequencing of Xenopus—The Highlights ................................................................................................. 157
10.2.1. Genome Sequencing of X. tropicalis ........................................................................................................ 157
10.2.2. Sequencing and Assembly of the X. laevis Genome................................................................................. 157
10.2.3. Comparison between X. tropicalis and X. laevis Genomes and Chromosomes........................................ 158
10.2.4. The Real Story of the Identifcation of L and S Subgenomes and Chromosomes .................................... 158
10.2.5. Asymmetrical Evolution of the L and S Subgenomes .............................................................................. 159
10.3. Studies Utilizing the Genome Sequences of Xenopus ............................................................................................. 161
10.3.1. W- and Z-Specifc Re gions in the Sex Chromosomes .............................................................................. 161
10.3.2. Analyses of Hox Genes............................................................................................................................. 162
10.3.3. Detailed Gene Organization in the Xenopus laevis Subgenomes ............................................................. 163
10.4. Conclusions.............................................................................................................................................................. 165
10.5. Future Directions ..................................................................................................................................................... 166
10.5.1. Comparative Genome Analysis ................................................................................................................. 166
10.5.2. Artif cial Hybrid Analysis ......................................................................................................................... 166
10.5.3. Artif cial Allopolyploid Analysis .............................................................................................................. 166
Acknowledgments ................................................................................................................................................................ 167
References............................................................................................................................................................................ 167
Clawed frogs of the genus Xenopus inhabit a large area of
Africa, where 29 extant species are currently recognized (as
of May 2021, https://amphibiaweb.org). Of them, the African
clawed frog Xenopus laevis was originally imported into
Europe from its native South Africa and has been used for
research in laboratories since the 1930s, initially mainly for
endocrinology studies and subsequently for developmental
biology research (reviewed in Gurdon and Hopwood, 2000),
and used as a model system to study cell cycle, oogenesis,
early development, and so on, by biochemical and molecular
biological approaches. X. laevis has various advantages as
a model animal, such as easy rearing and breeding, a wide
range of survival temperatures, resistance to infectious disease, and many others, which might be due to its allotetraploidy. However, from the late 1990s, when developmental in Kobel and Du Pasquier, 1986; Evans et al., 2004; Evans,
genetics started to dominate the feld of developmental
biology using knockout mice and mutagenesis screening
of zebrafsh, the allotetraploidy of X. laevis became a diswith a diploid Xenopus species, X. tropicalis, which has a
simpler genome and shorter generation time. X. tropicalis
was previously called Silurana tropicalis, but later Silurana
was treated as a subgenus; thus, this species was renamed
advantage. Therefore, scientists tried to replace X. laevis a single ancestral species is called autopolyploidy, whereas
Xenopus Silurana tropicalis, commonly called Xenopus
tropicalis. The genus Xenopus now consists of two subgenera, Xenopus and Silurana. Although X. tropicalis is a
suitable diploid model system in amphibians, X. laevis still
remains useful, and hence both X. tropicalis and X. laevis
have continued being used for research.
10.1. GENOME HISTORY OF THE
GENUS XENOPUS
The evolutionary history of Xenopus frogs leading to the
current phylogenetic relationships consist of bifurcating speciation and allopolyploidization by interspecies hybridization followed by polyploidization (Figure 10.1A) (reviewed
2008). Polyploidization is caused by duplication of the entire
genome, otherwise called whole genome duplication (WGD).
Polyploidy originating from duplication of a genome from
allopolyploidy refers to genome duplication of hybrid
genomes via interspecifc crossing, which is the case for
Xenopus species. Allotetraploid genomes, therefore, contain
two different genomes derived from diploid ancestor species,
DOI: 10.1201/9781003050230-12
155