Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource. 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. This protocol describes the application of in situ hic to the xenopus embryo. This genome encodes over 20,000 proteincoding genes, including orthologs of at least 1,700 human. A chromosomescale genome assembly and dense genetic map. Our reference database outperforms the provisional gene models based on genomic. A chromosomescale genome assembly and dense genetic map for. Nuclear assembly of purified crythecodinium cohnii. 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. Xenbase 1, the model organism database for xenopus laevis and tropicalis.
Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Homoeologous chromosomes of xenopus laevis are highly. Genomewide analysis of dorsal and ventral transcriptomes of the. Importance of xenopus tropicalis to biomedical and. Lab frog xenopus laevis genome sequence shows what happens. Regulatory remodeling in the allotetraploid frog xenopus. In the former, xenopus laevis has led the way in identifying the mechanisms of early fate decisions, patterning of the basic vertebrate body plan. Apr 29, 2010 harland and daniel rokhsar, colead of the xenopus genome project, uc berkeley biology professor and jgi scientist, have applied for a national institutes of health grant to sequence the x. The cdnas of the xgc project represent however less than 50% of the genes anticipated from the xenopus genome projects. 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. In particular, seamlessly combining data from two species, xenopus laevis a tetraploid, and xenopus tropicalis a diploid 2, in an integrated environment is complex.
Oct 31, 2007 the study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. Oct 24, 2017 genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Analysis of the considerable amount of est sequence. Chromatin immunoprecipitation and deep sequencing in. The array is comprised of more than 32,400 probe sets representing more than 29,900 x. African clawed frog xenopus laevis species profile. Manipulating the xenopusgenome with transposable elements. Here, we demonstrate the feasibility of deep genome free proteomics by using a reference proteome derived from heterogeneous mrna data.
Engineering xenopus embryos for phenotypic drug discovery. Xenopus tropicalis was introduced as a model system for genetic, and then genomic research, in the early 1990s, complementing work on the widely used model organism xenopus laevis. Nonetheless, some developmental mutations have been identified in. The authors also gratefully research support, grants ey019000 and ey017400 to rmg and grants dc010210, gm042341, and gm049346 to rmh. All resources generated by the xgc are publicly accessible to the. Accelerated gene evolution and subfunctionalization in the. Xenopus laevis is a popular amphibian model for studying vertebrate embryogenesis and. The western clawed frog xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid x. Royal society for the prevention of cruelty to animals, southwater, horsham, united kingdom. However, little is known about the consequences of this duplication at the level of the genome, the. The genome of xenopus tropicalis was sequenced in 2010 the first sequence of an amphibian. The solution came in the form of a close cousin of xenopus laevis, xenopus tropicalis. Its shorter generation time and diploid genome has facilitated a number of experimental approaches.
Guidance on the housing and care of the african clawed frog xenopus laevis. Importance of xenopus tropicalis to biomedical and biological research xenopus laevis is a unique resource for two critical areas in vertebrate biology. 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 genomic data and browser resources ncbi nih. Briefly, after fixing embryos with formaldehyde, nuclei are isolated and chromatin is digested with a. We identify more than 11,000 proteins with 99% confidence from the unfertilized xenopus laevis egg and estimate protein abundance with approximately 2fold precision. Harland and daniel rokhsar, colead of the xenopus genome project, uc berkeley biology professor and jgi scientist, have applied for a national institutes of health grant to sequence the x. The number of h3k4me3 peaks, dnamethylation free regions see. Fukui faculty of science and engineering, chuo univ.
Xenopus laevis has long been a popular model for studies of development and, based on the use of cell free extracts derived from its eggs, as a model for reconstitution of cell cycle regulation and other basic cellular processes. Hic is a sequencingbased method that captures threedimensional 3d genome interactions by counting the interaction frequencies of pairs of genomic loci. Xenopus genetics and husbandry issues arising in the creation of mutant lines both laevis and tropicalis will be used the goal is for you to practice the techniques using. Here we report a chromosomescale assembly of the x. At times the ponds that xenopus laevis is found in dry up, compelling it, in the dry season, to burrow into the mud, leaving a tunnel for air. Pdf complete replication of human sperm genome in egg. A relatively recent vertebrate genome duplication is that in xenopus laevis, which resulted.
Xenopus tropicalis v10 genome available to blast view on jbrowse. Sequential turnovers of sex chromosomes in african clawed. Cas9based genome editing in xenopus tropicalis request pdf. Pdf genome evolution in the allotetraploid frog xenopus laevis. The word xenopus means strange foot and laevis means smooth. However, work over the last several years has shown that intact xenopus eggs and. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of african clawed frogs genus xenopus. Therefore, proteomics studies can be routinely performed 6468. Xenortho db xenopus ortholog database is a database in which ortholog genes of xenopus tropicalis, xenopus laevis and humans are listed. Lab frog xenopus laevis genome sequence shows what happens when genomes collide. 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.
The african clawed frog xenopus laevis experienced a relatively recent tetraploidization 40 million years ago. Here we present a draft genome sequence assembly of x. Recent updates to the database include the xenopus laevis genome, a new xenopus tropicalis genome build, epigenomic data, collections of rna and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module. A xenopus tropicalis genome improvement grant and a xenopus laevis genome sequencing project are supported by grants gm086321 and hd065705, respectively, to rmh and daniel rokhsar. The complete nucleotide sequence of the xenopus laevis. The complete sequence of the 17,553nucleotide xenopus laevis mitochondrial genome has been determined. Genomewide expression profile of the response to spinal cord.
Genome evolution in the allotetraploid frog xenopus laevis. Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource project nbrp. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human. Xenopus laevis daudin, 1802, a new amphibian in portugal. Finally, ensembl incorporates biomart 12, which allows users to download. 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. Genes can also be obtained from source biosciences. The draft genome of the western clawed frog xenopus tropicalis, encoding over. African clawed frog got double the normal number of.
Genomewide expression profile of the response to spinal. We suggest using a current version of chrome, firefox, or safari. Generating a threedimensional genome from xenopus with hic. Xenopus laevis is a classical embryological and cellfree extract model system, but its genomic sequence had been lacking due to difficulties. Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Ecrbase offers downloadable files for promoter, synteny and ecrs. Regulatory remodeling in the allotetraploid frog xenopus laevis.
Xenopus cytogenetics and chromosomal evolution fulltext. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. Therefore, xenopus laevis 2n36 and xenopus silurana tropicalis 2n20 are good animal models for studying the process of genomic and chromosomal reorganization after wgd because x. The frog xenopus laevis has been an important model of vertebrate cell biology and development for many decades. Regions that are conserved at both the sequence level and at the. Here an international research collaboration reports the x. The senses of hearing and balance depend upon mechanoreception, a process that originates in. 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. Manipulating the xenopus genome with transposable elements. The recent completion of the xenopus laevis genome sequence combined with implementation of genome editing tools, such as talens transcription. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human disease genes. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a.
The assembly is a chromosome scale reassembly of version 7. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of this species. We use cookies to offer you a better experience, personalize content, tailor advertising, provide social media features, and better understand the use of our services. 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. Jan 11, 2018 reference genes are essential for gene expression analysis when using realtime quantitative pcr rtqpcr. This page contains links to sequence and annotation data downloads for the genome assemblies featured in the ucsc genome browser.
Introduction to xenopus xenbase a xenopus laevis and. Xenopus tropicalis as a model organism for genetics and. We notice that you are using internet explorer, which is not supported by xenbase and may cause the site to display incorrectly. The genome of the western clawed frog xenopus tropicalis. 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. Genetic research on xenopus laevis is challenged by its allotetraploid genome resulting from the hypothesized hybridization of two species yielding gene duplicates that would often preclude study of mutant phenotypes. So in summary, xenopus is a valuable tool because they are. It is incredibly hardy and can live up to 15 years. Here we reported the details of crythecodinium cohnii chromosomes being reconstituted in a cell free system of xenopus laevis eggs, followed by nuclear reassembly. 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. Xenopus laevis has regenerative and nonregenerative stages. At various points in its long history, the tractable xenopus embryo has been at the forefront of embryology, reprogramming biology, cell biology, and cell cycle research, but is only now emerging as a genomic organism.
The xenopus orfeome project was therefore launched in 2011 with the aim of developing cdna libraries containing all nonredundant orfs of both the x. Xenopus laevis is an essential model organism in several areas of biology see. Historically, the application of genome wide sequencing approaches to xenopus embryos, particularly to xenopus laevis, has been hampered by the lack of a. Complete replication of human sperm genome in egg extracts from xenopus laevis. This knowledgebase provides informatics resources, as well as genomic and biological data on xenopus frogs the mission of xenbase is to accelerate the translation of xenopus research into knowledge that will improve human health. Xenbase is a webaccessible model organism database mod. Genome evolution in the allotetraploid frog xenopus laevis nature. Genome editing workshop the national xenopus resource. A small, fastbreeding, diploid relative of the frog xenopus laevis, xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics. Reference genes are essential for gene expression analysis when using realtime quantitative pcr rtqpcr. 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. Its name is derived from the three short claws on each hind foot, which it uses to tear apart its food. 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.
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