Ncbi genome81 xenopus laevis ncbi assembly information. An international team of researchers has sequenced the genome of the western clawed frog, an important model animal in research on embryos and human genetic diseases. Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource. If you need corresponding gff files then getting the genome and gff3 files from xenbase may be better. Component name genome accessions component representation proteins. So in summary, xenopus is a valuable tool because they are.
The african clawed frog xenopus laevis, also known as the xenopus, african clawed toad, african clawtoed frog or the platanna is a species of african aquatic frog of the family pipidae. Using tractable organisms model systems to answer fundamental questions in medicine and biology is a common practice since the ancient years. An overview of using xenopus laevis as a model system. Within the endoderm, acts as an essential mediator of nodalnr1induced cardiogenesis in the overlying mesoderm. Xenbase continues to be the primary site for the xenopus genomes, managing gene name annotation and upgrading to a new genome browser jbrowse. Apr 29, 2010 an international team of researchers has sequenced the genome of the western clawed frog, an important model animal in research on embryos and human genetic diseases. Few studies have successfully used crispr in amphibians. The genome of xenopus tropicalis was sequenced in 2010 the first sequence of an amphibian.
Xenopus genomic data and browser resources sciencedirect. A xenopus tropicalis genome project advisory board was set up to insure an accurate and timely exchange of information between the jgi and the research community. Regulatory remodeling in the allotetraploid frog xenopus laevis. The frog xenopus laevis has been an important model of vertebrate cell biology and development for many decades. The solution came in the form of a close cousin of xenopus laevis, xenopus tropicalis. A nurd complex from xenopus laevis eggs is essential for. Xenopus laevis daudin, 1802, a new amphibian in portugal. Lab frog xenopus laevis genome sequence shows what happens. Apr 30, 2010 the western clawed frog xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the african clawed frog xenopus laevis with more tractable genetics. It nonetheless shares the embryological advantages of xenopus laevis and gene sequences are sufficiently similar that probes crossreact between the two species. The frog lays abundant eggs that are large, develop synchronously, and are easy to manipulate. Oct 24, 2017 genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Xenopus frog genome project on cbc doe joint genome. Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource project nbrp.
Multiple genome assemblies available for both species and transcriptomic and epigenetic. Mar 10, 2015 transcription in xenopus egg extract is sensitive to the dnatocytoplasm ratio to study the mechanism of zygotic genome activation in early embryos, we developed a cellfree system using xenopus laevis egg extracts that allowed us to directly manipulate the dnatocytoplasm ratio and measure the transcriptional response. Oct 19, 2016 the study, published in nature and featured on the cover, revealed that the x. In particular, seamlessly combining data from two species, xenopus laevis a tetraploid, and xenopus tropicalis a diploid 2, in an integrated environment is complex. The western clawed frog xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the african clawed frog xenopus laevis with more tractable genetics. Xenopus tropicalis v10 genome available to blast view on jbrowse. Xenopus tropicalis is a unique resource for two critical areas in vertebrate biology. However, little is known about the consequences of this duplication at the level of the genome, the. Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. Xenopus laevis is a popular amphibian model for studying vertebrate embryogenesis and. The allotetraploid frog, xenopus laevis, is commonly used to study developmental processes, but because of the presence of two homeologs for many genes, it has been difficult to use as a genetic model.
To explore the origins and consequences of tetraploidy in the african clawed frog, we sequenced the xenopus laevis genome and compared it to the related diploid x. The complete sequence of the 17,553nucleotide xenopus laevis mitochondrial genome has been determined. The senses of hearing and balance depend upon mechanoreception, a process that originates in. During xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. Fukui faculty of science and engineering, chuo univ. Xenortho db xenopus ortholog database is a database in which ortholog genes of xenopus tropicalis, xenopus laevis and humans are listed. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human. The xenopus gene collection xgc is an nih initiative that supports the production of cdna libraries, clones and 53 sequences to provide a set of fulllength open reading frame sequences and cdna clones of expressed genes for xenopus laevis and xenopus tropicalis. The frog xenopus laevis has been used to study early stages of vertebrate development for more than 50 years and continues to be an important model system. International xenopus sequencing consortium assembly date. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. The complete nucleotide sequence of the xenopus laevis. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of this species. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates.
Genome organization of the vg1 and nodal3 gene clusters in. Manipulating the xenopus genome with transposable elements. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human disease genes. Royal society for the prevention of cruelty to animals, southwater, horsham, united kingdom.
Xenopus is also a unique system for analyses of genome evolution and whole genome duplication in vertebrates, as different xenopus species form a ploidy series formed by interspecific hybridization. Data is collected from other databases, highthroughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis. Here, we show that the vg1 and nodal3 genes of xenopus laevis are present in gene clusters on chromosomes xla1l and xla3l, respectively, and that both gene clusters have been completely lost from the syntenic s chromosome regions. We added varying concentrations of purified sperm chromatin. The african clawed frog xenopus laevis experienced a relatively recent tetraploidization 40 million years ago.
A relatively recent vertebrate genome duplication is that in xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. One of the model systems with important contributions is xenopus laevis, the african clawed frog, a pseudotetraploid vertebrate which lives in. Contributions in cell biology and biochemistry include seminal work on chromosome. Analysis of the considerable amount of est sequence. Although biologists have uncovered the dna sequences of more than 175 organisms so far from corn to the spotted green puffer fish this is the first genome. Xenbase has been available since 1999, and covers both x. The study, published in nature and featured on the cover, revealed that the x.
There is a wealth of data in the literature on gene function, fulllength cdna sequences and in situ databases on laevis, but no genome sequence or genetics. Data is collected from other databases, highthroughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature. Additional information such as the elucidatedsequences and their gene models descriptions including intron and exon positions of each gene and the start and end of transcripts can be viewed from multiple websites, including the above xenopus. Introduction to xenopus xenbase a xenopus laevis and. Oct 20, 2016 to explore the origins and consequences of tetraploidy in the african clawed frog, we sequenced the xenopus laevis genome and compared it to the related diploid x. Transcription in xenopus egg extract is sensitive to the dnatocytoplasm ratio to study the mechanism of zygotic genome activation in early embryos, we developed a cellfree system using xenopus laevis egg extracts that allowed us to directly manipulate the dnatocytoplasm ratio and measure the transcriptional response. The two bestknown species of this genus are xenopus laevis and xenopus tropicalis, which are commonly studied as model organisms for developmental biology. Apr 29, 2010 the highquality draft sequence of the genome of x. The genome sequences of xenopus tropicalis and its related species xenopus laevis have been sequenced and published by international genome projects. Guidance on the housing and care of the african clawed frog xenopus laevis. The xenopus laevis genome encodes a frog whose cells and body size are larger than those with smaller genomes.
Ncbi assembly779791 international xenopus sequencing consortium bioproject information. Accelerated gene evolution and subfunctionalization in the. The western clawed frog xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the african clawed frog xenopus laevis with more tractable. All resources generated by the xgc are publicly accessible to the biomedical research community. In addition to the key attributes of these embryos for in vivo imaging, cellfree extracts from xenopus provide among the most powerful in vitro systems for studies of cell and molecular biology. How the african clawed frog got an extra pair of genes. The two species of xenopus most commonly used in biomedical research are the diploid xenopus silurana tropicalis and the tetraploid xenopus laevis. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. Genome evolution in the allotetraploid frog xenopus laevis. Oct 19, 2016 to explore the origins and consequences of tetraploidy in the african clawed frog, we sequenced the xenopus laevis genome and compared it to the related diploid x.
In the former, xenopus laevis has led the way in identifying the mechanisms of early fate decisions, patterning of the basic vertebrate body plan. Generation of a xenopus laevis f1 albino j strain by genome editing and oocyte hosttransfer wil ratzan, rosalia falco, cristy salanga, matthew salanga, marko e. Reference gene identification and validation for quantitative. They demonstrate that xnurd can initiate dna replication in the absence of noncoding y rnas, which only become essential for.
African clawed frog xenopus laevis species profile. In the former, xenopus laevis has led the way in identifying the mechanisms of early fate decisions, patterning of the basic vertebrate body plan, and early organogenesis. Here we present a draft genome sequence assembly of x. The array is comprised of more than 32,400 probe sets representing more than 29,900 x. Histone titration against the genome sets the dnato. Tissuespecific gene inactivation in xenopus laevis. African clawed frog genome contains two full sets of. Genome evolution in the allotetraploid frog xenopus laevis nature. Its name is derived from the three short claws on each hind foot, which it uses to tear apart its food. Dynamics of the genome during early xenopus laevis. Genetic manipulation of this tractable model system would further enhance the use of the frog in developmental studies. The common laboratory frog xenopus laevis has puzzled researchers because it has twice the normal number of genes. The word xenopus means strange foot and laevis means smooth.
Importance of xenopus tropicalis to biomedical and. In 1931, lancelot hogben noted that xenopus laevis females ovulated when injected with the urine of pregnant women. Reference genes are essential for gene expression analysis when using realtime quantitative pcr rtqpcr. Xenopus frog genome project on cbc doe joint genome institute. Few studies have successfully used crispr in amphibians, and. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Inhibits wnt, nodalnr1 and bmp signaling in the embryo to promote head formation and anterior neural induction.
6 511 1368 990 328 1148 629 811 20 1028 491 773 1013 455 574 474 1104 653 1574 552 742 1100 178 843 826 1258 1034 1391 257 268 1035 531 554 1503 1322 816 1190 1055 295 511 1014 1069 373 52 385 190