161
Continuing Evolution of Xenopus Genome
FIGURE 10.1 (Continued)
from Session et al. (2016 ) are indicated. Phylogenetic relationships of Xenopus species are adopted from Evans et al. (2004). Species
of Xenopus other than those of subgenus Silurana (including X. epitropicalis and X. tropicalis) belong to the subgenus Xenopus. X.
ruwenzoriensis speciated by hybridization between X. amieti and X. pygmaeus followed by polyploidization (dotted lines with arrow).
(B) Orthologous and homeologous relationships between X. tropicalis chromosomes (XTR) and X. laevis (XLA) L (long) and S (short)
chromosomes based on chromosome-scale sequence assembly and BAC FISH data. XLA9L and XLA9S are also called XLA9_10L and
XLA9_10S, which correspond to XTR9 and XTR10 due to chromosome fusion. XLA2L corresponds to both Z and W chromosomes.
(C) Schematic representation of the fate of transposons. Transposons can be horizontally transferred into a genome, then increase their
number to invade the entire genome (expansion). Meanwhile, transposons become inactivated by a host immune system and the inactivated transposons, called fossil transposons, are gradually mutated over time (t). (D) Allotetraploidization and subgenome specif c fossil
transposons in the X. laevis lineage. L- and S-specifc fossil transposons (TpL and TpS, respectively) were identifed in X. laevis. (E)
FISH analysis with the TpS probe. Either homeologous chromosome pair is labeled (magenta). Notably, TpS-positive chromosomes are
found to be the shorter chromosome in each homologous pair, leading to the idea that each of longer (L) and shorter (S) chromosome sets
corresponds to either of the parental chromosome sets.
Source: Panels B and E were copied from Session et al. (2016).
Overall, the two subgenomes evolved differently, with the
L subgenome conserving sequences of the ancestral species
and the S subgenome having a higher percentage of broken genes due to deletions and rearrangements. Thus, we
showed for the frst time that the subgenomes in an allotetraploid evolve asymmetrically. Diploidization is the process in
which polyploids become diploid, and the loss of homeologous genes that is observed in X. laevis is probably an early
event in diploidization. However, it still remains unclear
what the main evolutionary force driving the differences
between the L and S subgenomes was.
10.3. STUDIES UTILIZING THE GENOME
SEQUENCES OF XENOPUS
Further precise studying of the whole genome led to a series of
new fndings to understand the changes in the X. laevis genome
after allotetraploidization. Individual studies were performed
by different groups, focusing on the sex determining Z and W
loci, Hox clusters, tandemly repeated genes, gene families, and
so on in the genomes of X. laevis and X. tropicalis.
10.3.1. W- AND Z-SPECIFIC REGIONS IN
THE SEX CHROMOSOMES
The sex of X. laevis is determined by a ZZ-ZW chromosomal
system, in which females are heterogametic, as identif ed by
genetic analysis (Chang and Witschi, 1956). The sex-determining gene, DM-W (the same as dmw), which is female
specifc and thus is on the W-chromosome, was identif ed in
2008 (Yoshimoto et al., 2008). This gene is one of the members of the dmrt family, whose members are known to be
involved in sexual development, such as Drosophila melanogaster doublesex (dsx), Caenorhabditis elegans mab-3,
and Mus musculus dmrt1. The sex chromosomes of X.
laevis were not identifed for a long time, but from FISH
analysis using dmw as a probe, a single W-chromosome was
distinguished and dmw was located at the q-subtelomeric
region (Yoshimoto et al., 2008). The sex chromosome is
XLA2L, but there are two versions: the one containing dmw
is the W-chromosome, and the other lacking dmw is the
Z-chromosome.
To identify possible W or Z region-containing clones, a
fosmid library was screened by colony hybridization with
dmw -fanking sequences as probes. These clones were analyzed for the presence of dmw. A number of these clones
with or without dmw and BACs in this region were chosen
for full sequencing (Session et al., 2016; Mawaribuchi et al.,
2017). Using the full sequences of these clones helped to
correct the mistakes in the computational ver. 9.1 assembly
of the X. laevis genome and revealed the structure of the Wor Z-specifc regions. The W-specifc sequence containing
dmw is 278 kb in length, whereas the Z-specif c sequence
is 83 kb ( Figure 10.2A) ( Mawaribuchi et al., 2017). In total,
three W-specifc genes including dmw and one Z-specif c
gene were found (Figure 10.2A). Comparisons of these
genes with their autosomal homologous genes/sequences in
X. laevis and X. tropicalis were performed to clarify their
evolutionary histories. The result for dmw was consistent
with previous reports that dmw may have emerged as a
duplicate of the dmrt1 gene (Yoshimoto et al., 2008), to be
specifc, from dmrt1.S (reported as dmrt1β) (Bewick et al.,
2010) on XLA1S, and integrated into the XLA2L chromosome. The other two W-specifc and one Z-specif c genes
were suggested to be duplicates from homologous counterparts on the L chromosomes, but from separate chromosomes. Therefore, it appears that all four W- or Z-specif c
genes were integrated independently. Interestingly, dmw is
not found in X. tropicalis (Yoshimoto et al., 2008) nor in
X. borealis (Bewick et al., 2010). This suggests that dmw
emerged after the divergence of X. laevis and X. borealis or
was lost in the X. borealis lineage and that sex-determination
mechanisms of related species are different.
A similar situation is found in the f sh Oryzias latipes,
whose male sex-determining gene isdmy/dmrt1bY( Matsuda
et al., 2002; Nanda et al., 2002), which arose evolutionarily
as a duplicated version of the autosomal dmrt1 gene.
This gene is, however, not the universal sex-determining
gene in the genus Oryzias (Kondo et al., 2003; Kondo
et al., 2004). These examples demonstrate the variability
of sex-determining systems. It would be quite interesting to identify the sex-determining genes of X. tropicalis
and X. borealis as well as other Xenopus species to learn
about the evolution of sex determination in Xenopus.
Continuing Evolution of Xenopus Genome
FIGURE 10.1 (Continued)
from Session et al. (2016 ) are indicated. Phylogenetic relationships of Xenopus species are adopted from Evans et al. (2004). Species
of Xenopus other than those of subgenus Silurana (including X. epitropicalis and X. tropicalis) belong to the subgenus Xenopus. X.
ruwenzoriensis speciated by hybridization between X. amieti and X. pygmaeus followed by polyploidization (dotted lines with arrow).
(B) Orthologous and homeologous relationships between X. tropicalis chromosomes (XTR) and X. laevis (XLA) L (long) and S (short)
chromosomes based on chromosome-scale sequence assembly and BAC FISH data. XLA9L and XLA9S are also called XLA9_10L and
XLA9_10S, which correspond to XTR9 and XTR10 due to chromosome fusion. XLA2L corresponds to both Z and W chromosomes.
(C) Schematic representation of the fate of transposons. Transposons can be horizontally transferred into a genome, then increase their
number to invade the entire genome (expansion). Meanwhile, transposons become inactivated by a host immune system and the inactivated transposons, called fossil transposons, are gradually mutated over time (t). (D) Allotetraploidization and subgenome specif c fossil
transposons in the X. laevis lineage. L- and S-specifc fossil transposons (TpL and TpS, respectively) were identifed in X. laevis. (E)
FISH analysis with the TpS probe. Either homeologous chromosome pair is labeled (magenta). Notably, TpS-positive chromosomes are
found to be the shorter chromosome in each homologous pair, leading to the idea that each of longer (L) and shorter (S) chromosome sets
corresponds to either of the parental chromosome sets.
Source: Panels B and E were copied from Session et al. (2016).
Overall, the two subgenomes evolved differently, with the
L subgenome conserving sequences of the ancestral species
and the S subgenome having a higher percentage of broken genes due to deletions and rearrangements. Thus, we
showed for the frst time that the subgenomes in an allotetraploid evolve asymmetrically. Diploidization is the process in
which polyploids become diploid, and the loss of homeologous genes that is observed in X. laevis is probably an early
event in diploidization. However, it still remains unclear
what the main evolutionary force driving the differences
between the L and S subgenomes was.
10.3. STUDIES UTILIZING THE GENOME
SEQUENCES OF XENOPUS
Further precise studying of the whole genome led to a series of
new fndings to understand the changes in the X. laevis genome
after allotetraploidization. Individual studies were performed
by different groups, focusing on the sex determining Z and W
loci, Hox clusters, tandemly repeated genes, gene families, and
so on in the genomes of X. laevis and X. tropicalis.
10.3.1. W- AND Z-SPECIFIC REGIONS IN
THE SEX CHROMOSOMES
The sex of X. laevis is determined by a ZZ-ZW chromosomal
system, in which females are heterogametic, as identif ed by
genetic analysis (Chang and Witschi, 1956). The sex-determining gene, DM-W (the same as dmw), which is female
specifc and thus is on the W-chromosome, was identif ed in
2008 (Yoshimoto et al., 2008). This gene is one of the members of the dmrt family, whose members are known to be
involved in sexual development, such as Drosophila melanogaster doublesex (dsx), Caenorhabditis elegans mab-3,
and Mus musculus dmrt1. The sex chromosomes of X.
laevis were not identifed for a long time, but from FISH
analysis using dmw as a probe, a single W-chromosome was
distinguished and dmw was located at the q-subtelomeric
region (Yoshimoto et al., 2008). The sex chromosome is
XLA2L, but there are two versions: the one containing dmw
is the W-chromosome, and the other lacking dmw is the
Z-chromosome.
To identify possible W or Z region-containing clones, a
fosmid library was screened by colony hybridization with
dmw -fanking sequences as probes. These clones were analyzed for the presence of dmw. A number of these clones
with or without dmw and BACs in this region were chosen
for full sequencing (Session et al., 2016; Mawaribuchi et al.,
2017). Using the full sequences of these clones helped to
correct the mistakes in the computational ver. 9.1 assembly
of the X. laevis genome and revealed the structure of the Wor Z-specifc regions. The W-specifc sequence containing
dmw is 278 kb in length, whereas the Z-specif c sequence
is 83 kb ( Figure 10.2A) ( Mawaribuchi et al., 2017). In total,
three W-specifc genes including dmw and one Z-specif c
gene were found (Figure 10.2A). Comparisons of these
genes with their autosomal homologous genes/sequences in
X. laevis and X. tropicalis were performed to clarify their
evolutionary histories. The result for dmw was consistent
with previous reports that dmw may have emerged as a
duplicate of the dmrt1 gene (Yoshimoto et al., 2008), to be
specifc, from dmrt1.S (reported as dmrt1β) (Bewick et al.,
2010) on XLA1S, and integrated into the XLA2L chromosome. The other two W-specifc and one Z-specif c genes
were suggested to be duplicates from homologous counterparts on the L chromosomes, but from separate chromosomes. Therefore, it appears that all four W- or Z-specif c
genes were integrated independently. Interestingly, dmw is
not found in X. tropicalis (Yoshimoto et al., 2008) nor in
X. borealis (Bewick et al., 2010). This suggests that dmw
emerged after the divergence of X. laevis and X. borealis or
was lost in the X. borealis lineage and that sex-determination
mechanisms of related species are different.
A similar situation is found in the f sh Oryzias latipes,
whose male sex-determining gene isdmy/dmrt1bY( Matsuda
et al., 2002; Nanda et al., 2002), which arose evolutionarily
as a duplicated version of the autosomal dmrt1 gene.
This gene is, however, not the universal sex-determining
gene in the genus Oryzias (Kondo et al., 2003; Kondo
et al., 2004). These examples demonstrate the variability
of sex-determining systems. It would be quite interesting to identify the sex-determining genes of X. tropicalis
and X. borealis as well as other Xenopus species to learn
about the evolution of sex determination in Xenopus.