Genome evolution in the allotetraploid frog xenopus laevis. 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. Genome editing workshop the national xenopus resource. African clawed frog xenopus laevis species profile. Genes can also be obtained from source biosciences.
Xenopus cytogenetics and chromosomal evolution fulltext. Here, we demonstrate the feasibility of deep genome free proteomics by using a reference proteome derived from heterogeneous mrna data. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human disease genes. A chromosomescale genome assembly and dense genetic map for.
Introduction to xenopus xenbase a xenopus laevis and. The western clawed frog xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid x. 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. In the former, xenopus laevis has led the way in identifying the mechanisms of early fate decisions, patterning of the basic vertebrate body plan. Xenbase is a webaccessible model organism database mod. Royal society for the prevention of cruelty to animals, southwater, horsham, united kingdom. Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource. Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Xenbase 1, the model organism database for xenopus laevis and tropicalis. Xenopus laevis is an essential model organism in several areas of biology see.
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. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of this species. 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. Briefly, after fixing embryos with formaldehyde, nuclei are isolated and chromatin is digested with a. Hic is a sequencingbased method that captures threedimensional 3d genome interactions by counting the interaction frequencies of pairs of genomic loci.
The cdnas of the xgc project represent however less than 50% of the genes anticipated from the xenopus genome projects. 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. Therefore, proteomics studies can be routinely performed 6468. 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. Importance of xenopus tropicalis to biomedical and biological research xenopus laevis is a unique resource for two critical areas in vertebrate biology. Xenortho db xenopus ortholog database is a database in which ortholog genes of xenopus tropicalis, xenopus laevis and humans are listed. A chromosomescale genome assembly and dense genetic map. 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. Nuclear assembly of purified crythecodinium cohnii. Pdf complete replication of human sperm genome in egg. Regions that are conserved at both the sequence level and at the. Xenopus laevis is a classical embryological and cellfree extract model system, but its genomic sequence had been lacking due to difficulties. The number of h3k4me3 peaks, dnamethylation free regions see.
Manipulating the xenopus genome with transposable elements. Here an international research collaboration reports the x. Lab frog xenopus laevis genome sequence shows what happens when genomes collide. The genome of xenopus tropicalis was sequenced in 2010 the first sequence of an amphibian. 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. Fukui faculty of science and engineering, chuo univ. It is incredibly hardy and can live up to 15 years. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates.
A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a. Here we present a draft genome sequence assembly of x. The draft genome of the western clawed frog xenopus tropicalis, encoding over. Jan 11, 2018 reference genes are essential for gene expression analysis when using realtime quantitative pcr rtqpcr. We identify more than 11,000 proteins with 99% confidence from the unfertilized xenopus laevis egg and estimate protein abundance with approximately 2fold precision.
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. 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. 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. Xenopus laevis has regenerative and nonregenerative stages. Our reference database outperforms the provisional gene models based on genomic. The solution came in the form of a close cousin of xenopus laevis, xenopus tropicalis. All resources generated by the xgc are publicly accessible to the. Engineering xenopus embryos for phenotypic drug discovery. Lab frog xenopus laevis genome sequence shows what happens. Xenopus laevis is a popular amphibian model for studying vertebrate embryogenesis and. Oct 31, 2007 the study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. The genome of the western clawed frog xenopus tropicalis.
Xenopus laevis daudin, 1802, a new amphibian in portugal. Ecrbase offers downloadable files for promoter, synteny and ecrs. 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. Xenopus tropicalis v10 genome available to blast view on jbrowse. The complete sequence of the 17,553nucleotide xenopus laevis mitochondrial genome has been determined. The authors also gratefully research support, grants ey019000 and ey017400 to rmg and grants dc010210, gm042341, and gm049346 to rmh. Finally, ensembl incorporates biomart 12, which allows users to download. The african clawed frog xenopus laevis experienced a relatively recent tetraploidization 40 million years ago. The array is comprised of more than 32,400 probe sets representing more than 29,900 x. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of african clawed frogs genus xenopus. The assembly is a chromosome scale reassembly of version 7.
This genome encodes over 20,000 proteincoding genes, including orthologs of at least 1,700 human. Accelerated gene evolution and subfunctionalization in the. The word xenopus means strange foot and laevis means smooth. Genomewide expression profile of the response to spinal. A relatively recent vertebrate genome duplication is that in xenopus laevis, which resulted. African clawed frog got double the normal number of. The complete nucleotide sequence of the xenopus laevis. Xenopus gene collection national institutes of health. 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 senses of hearing and balance depend upon mechanoreception, a process that originates in. 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.
Importance of xenopus tropicalis to biomedical and. Manipulating the xenopusgenome with transposable elements. 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 xenopus orfeome project was therefore launched in 2011 with the aim of developing cdna libraries containing all nonredundant orfs of both the x. So in summary, xenopus is a valuable tool because they are. Chromatin immunoprecipitation and deep sequencing in. Guidance on the housing and care of the african clawed frog xenopus laevis. We suggest using a current version of chrome, firefox, or safari. However, little is known about the consequences of this duplication at the level of the genome, the. If you need corresponding gff files then getting the genome and gff3 files from xenbase may be better. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. 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. Reference genes are essential for gene expression analysis when using realtime quantitative pcr rtqpcr.
Pdf genome evolution in the allotetraploid frog xenopus laevis. Regulatory remodeling in the allotetraploid frog xenopus laevis. 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. Sequential turnovers of sex chromosomes in african clawed. Historically, the application of genome wide sequencing approaches to xenopus embryos, particularly to xenopus laevis, has been hampered by the lack of a. Xenopus genomic data and browser resources ncbi nih. Reference gene identification and validation for quantitative. Homoeologous chromosomes of xenopus laevis are highly. In addition to the key attributes of these embryos for in vivo imaging, cell free extracts from xenopus provide among the most powerful in vitro systems for studies of cell and molecular biology. 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. 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. A small, fastbreeding, diploid relative of the frog xenopus laevis, xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics.
Here we report a chromosomescale assembly of the x. 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. Xenopus tropicalis as a model organism for genetics and. Regulatory remodeling in the allotetraploid frog xenopus. 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. Here we reported the details of crythecodinium cohnii chromosomes being reconstituted in a cell free system of xenopus laevis eggs, followed by nuclear reassembly. Amphibian research center through collaboration between the xenopus community in japan xcij and national bioresource project nbrp. 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 recent completion of the xenopus laevis genome sequence combined with implementation of genome editing tools, such as talens transcription.
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. Generating a threedimensional genome from xenopus with hic. Oct 24, 2017 genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Genomewide expression profile of the response to spinal cord. Its shorter generation time and diploid genome has facilitated a number of experimental approaches. The frog xenopus laevis has been an important model of vertebrate cell biology and development for many decades. However, work over the last several years has shown that intact xenopus eggs and. Its name is derived from the three short claws on each hind foot, which it uses to tear apart its food. This page contains links to sequence and annotation data downloads for the genome assemblies featured in the ucsc genome browser. 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. We notice that you are using internet explorer, which is not supported by xenbase and may cause the site to display incorrectly. This genome encodes more than 20,000 proteincoding genes, including orthologs of at least 1700 human.
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