Xenopus tropicalis: An Ideal Experimental Animal in Amphibia

Kashiwagi, Kazuhiro; Kashiwagi, Akihiko; Kurabayashi, Atsushi; Hanada, Hideki; Nakajima, Keisuke; Okada, Morihiro; Takase, Miyuki; Yaoita, Yoshio

doi:10.1538/expanim.59.395

Cited by 60 publications

(46 citation statements)

References 38 publications

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“…Xenopus tropicalis individuals were provided by the National Bioresource Project, Japan (Kashiwagi et al 2010). DNA was extracted from the animals using a previously described method (Hikosaka et al 2000).…”

Section: Animalsmentioning

confidence: 99%

Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

et al. 2011

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To investigate the recent transposition activity of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis (Western clawed frog), we analyzed the intraspecific polymorphisms associated with MITE insertion in X. tropicalis for three subfamilies of the T2 family (T2-A1, T2-C, and T2-E). A high frequency of MITE-insertion polymorphisms was observed at the T2-A1 (50%) and T2-C insertion loci (60%), but none were noted at the T2-E insertion locus (0%). Analyses of the collected data indicated that members of the T2-A1 and T2-C subfamilies may be currently active in the host species. Identification of these active transpositions will help us in understanding the mechanisms underlying the long-term survival (over several tens of millions of years) of the T2-A1 and T2-C subfamilies.

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Section: Animalsmentioning

confidence: 99%

Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

et al. 2011

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“…This model system is particularly valuable for studies of early vertebrate embryonic development [3,4], functional genomics [5,6], cell biology [3,7], and vertebrate genome evolution [8]. Its 1.7 × 10 9 bp genome was sequenced [9] and a genetic map covering its 10 chromosomes was constructed [10].…”

Section: Introductionmentioning

confidence: 99%

Efficient high-throughput sequencing of a laser microdissected chromosome arm

Seifertova

Zimmerman²,

Gilchrist³

et al. 2013

BMC Genomics

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BackgroundGenomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly.ResultsWe laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly.ConclusionWe present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds.

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“…Two species belonging to the genus Xenopus (Xenopus laevis and Xenopus tropicalis) are fully aquatic anurans and morphologically similar to each other (17); however, the optimal temperature range for each of these two species is quite different. The optimal temperature range of X. laevis is 16 -22°C, whereas that of X. tropicalis is 22-28°C (18,19). Furthermore, X. laevis inhabits cooler regions compared with X. tropicalis, found in Africa, and thus these two Xenopus species have adapted to different thermal niches (17).…”

mentioning

confidence: 99%

Evolution of Heat Sensors Drove Shifts in Thermosensation between Xenopus Species Adapted to Different Thermal Niches

Saito

Ohkita

Saito

et al. 2016

Journal of Biological Chemistry

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Temperature is one of the most critical environmental factors affecting survival, and thus species that inhabit different thermal niches have evolved thermal sensitivities suitable for their respective habitats. During the process of shifting thermal niches, various types of genes expressed in diverse tissues, including those of the peripheral to central nervous systems, are potentially involved in the evolutionary changes in thermosensation. To elucidate the molecular mechanisms behind the evolution of thermosensation, thermal responses were compared between two species of clawed frogs (Xenopus laevis and Xenopus tropicalis) adapted to different thermal environments. X. laevis was much more sensitive to heat stimulation than X. tropicalis at the behavioral and neural levels. The activity and sensitivity of the heat-sensing TRPA1 channel were higher in X. laevis compared with those of X. tropicalis. The thermal responses of another heat-sensing channel, TRPV1, also differed between the two Xenopus species. The species differences in Xenopus TRPV1 heat responses were largely determined by three amino acid substitutions located in the first three ankyrin repeat domains, known to be involved in the regulation of rat TRPV1 activity. In addition, Xenopus TRPV1 exhibited drastic species differences in sensitivity to capsaicin, contained in chili peppers, between the two Xenopus species. Another single amino acid substitution within Xenopus TRPV1 is responsible for this species difference, which likely alters the neural and behavioral responses to capsaicin. These combined subtle amino acid substitutions in peripheral thermal sensors potentially serve as a driving force for the evolution of thermal and chemical sensation.Animals have evolved sophisticated physiological systems for sensing ambient temperatures, as fluctuations in environmental temperature significantly affect various biological processes. Species adapted to different thermal niches are likely to have acquired specific thermal sensitivities suitable for their respective habitats. Recent progress and understanding of the molecular mechanisms behind thermosensation has enabled us to elucidate the molecular basis for the evolution of thermosensation in the process of shifting thermal niches (1-3).In vertebrates, peripheral sensory neurons such as dorsal root ganglion (DRG) 3 and trigeminal ganglion neurons relay temperature information to the central nervous system. During the initiation of signal transduction, thermal stimuli are transduced into electrical signals and a subset of ion channels that are thermally activated plays crucial roles in this process. These ion channels belong to the transient receptor potential (TRP) ion channel superfamily and are called "thermoTRP" (1-3). Animals possess several kinds of thermoTRP channels, which have distinctive temperature ranges for activation. For example, TRPV1 is activated by heat (4 -7), whereas TRPM8 is activated by cold (1-3, 8).Temperature sensitivity among orthologous thermoTRP channels has changed duri...

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Xenopus tropicalis: An Ideal Experimental Animal in Amphibia

Cited by 60 publications

References 38 publications

Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

Efficient high-throughput sequencing of a laser microdissected chromosome arm

Evolution of Heat Sensors Drove Shifts in Thermosensation between Xenopus Species Adapted to Different Thermal Niches

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