Xenopus laevis is an important vertebrate model in developmental and cell biology that has experienced a recent WGD (~40 million years ago [MYA], based on cDNA alignments (Hellsten, 2007). You can download X. laevis genomes at XenBase FTP site. In fact, Xenopus has become a major vertebrate model for the cellular and developmental biology research that is supported by most of the Institutes of the NIH. Initially, at the beginning of the 2000s, the tetraploid genome was thought to bring about problems that would not be observed if the diploid Xenopus tropicalis was chosen for sequencing. Major funding for Xenbase is provided by grant P41 HD064556. husbandry, cell biology, imaging, genetics, transgenesis, genomics). About the XGC. I want to use Galaxy to analyze some RNA-seq data in the near future and would appreciate it if the Galaxy team could upload the Xenopus laevis reference genome! We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 … Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … 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. tropicalis genome… The frog Xenopus laevis has been an important model of vertebrate cell biology and development for many decades. Xenopus laevis (v9.1 genome assembly) L sub-genome, and (iii) XLA.S: X. laevis S sub-genome. While Xenopus laevis is the most commonly used species for developmental biology studies, genetic studies, especially forward genetic studies, can be complicated by their pseudotetraploid genome. The genomes of both X. laevis and X. tropicalis have been sequenced. Mission Statement: The National Xenopus Resource (NXR) is located at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, and serves as a national stock center for X. laevis and X. tropicalis as well as a training center for advanced technologies (e.g. Molecular cloning of X. laevis urocortins We searched the Xenopus tropicalis genome database (assembly version 1.0; Joint Genome Institute, Walnut Creek, CA; release date, December 10, 2003) using the TBLASTN protocol with amino acid sequences of the prohormones of goldfish urotensin I … The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. Alternatively, you can download them at UTA 'daudin' web repository. Xenopus laevis (African clawed frog) Genome info Pathway map Brite hierarchy Module Genome map Blast Taxonomy: Search genes: KEGG pathway maps Metabolism. This subspecies has a fifth toe that is much longer than the tibia. Several features make Xenopus eggs and embryos an outstanding tool in biomedical research. Studying model organisms, such as Xenopus, allows us to decipher how regulatory and interactions networks direct embryonic development, how they adapt during aging and under environmental stress, and how they become dysregulated to cause disease, malformations and birth defects. For example, I renamed 'Scaffold102974' in XenBase/JGI 7.1 genome to 'JGIv7b.000102974'. Genomes were aligned using Synteny Mapping and Analysis Program (SyMAP) v 4.2 [ … 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. They display remarkable structural similarity with the human genome (Hellsten et al. A complete sequence of the X. laevis genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory regions, and for design of morpholino-oligonucleotides for gene knockdowns. it has four sets of chromosomes), thus X.tropicalis is a more simple model for genetic studies. Genome evolution in the allotetraploid frog Xenopus laevis. Session et al. The array is comprised of more than 32,400 probe sets representing more than 29,900 X. laevis transcripts, and was designed in close collaboration with the Xenopus research community as part of the GeneChip Consortia Program. Finally, the development and utilization of novel technologies for loss-of-function and genome editing combined with transgenesis as well as availability of transgenic lines with various cell types expressing fluorescence reporters further empower Xenopus as a research platform for immunological research. About the XGC. 90% Identity; 50% Identity; Cross-references i … ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. 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. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. As pets. Texas Institute for Drug and Diagnostic Development, University of Texas Genome Sequencing and Analysis facility, http://daudin.icmb.utexas.edu/XENLA_JGIv72/, http://daudin.icmb.utexas.edu/XENTR_JGIv80/, http://gbrowse.xenbase.org/fgb2/gbrowse/xl7_1/, http://gbrowse.xenbase.org/fgb2/gbrowse/xt8_0/, http://daudin.icmb.utexas.edu/Oktoberfest/, http://hubble.icmb.utexas.edu/index.php?title=Xenopus_Genome_Project&oldid=1843, Attribution-Noncommercial-No Derivative Works 3.0 Unported. 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. 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. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc., as initially identified by the group of Jan-Fang Cheng via probing the CHORI-219 library), as well as 10 BACs that have already been sequenced by the DOE Joint Genome Institute/HudsonAlpha Genome Sequencing Center to serve as positive controls for the sequencing and assembly pipeline. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. To clone the first anion channel from Xenopus laevis (X. laevis), we isolated a calcium-activated chloride channel (CLCA)-like membrane protein 6 gene (CMP6) in X. laevis.As a first step in gene isolation, an expressed sequence tags database was screened to find the partial cDNA fragment. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. Sperm contribute genetic and epigenetic information to the embryo. "Development version" of Xenopus gene annotation, with JBrowse genome browser (Here is short intro if you want to mirror this site, or host your own Xenopus genome browser). Session et al. They display remarkable structural similarity with the human genome (Hellsten et al. Comparing the two species, X.tropicalis has a much shorter life cycle than does X. laevis, growing to adult in 4 months compared with 12 months, making it a faster system to study. Xenbase: The Xenopus Model Organism Knowledgebase. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. The genomes of both X. laevis and X. tropicalis species have been sequenced and display remarkable structural similarity with the human genome, meaning that findings from Xenopus provide insights into many human conditions and diseases. We're posting our intermediate datasets here in advance of publication for use by the wider community. Fortunately, a closely related frog, Xenopus tropicalis, has a more amenable diploid genome and it also retains the same advantages as Xenopus laevis. Xenopus are an invaluable tool to study vertebrate embryology and development, basic cell and molecular biology, genomics, neurobiology and toxicology and to model human diseases. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. The genomes of both X. laevis and X. tropicalis have been sequenced. Xenopus is a genus of African frogs that are commonly known as the African clawed frogs. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Egg production can be stimulated by injection of chorionic gonadotropin. During Xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. Hello! Here we present a draft genome sequence assembly of X. tropicalis . Periodic albino mutant X. laevis may be a useful model in studying this human syndrome. This page was last modified on 14 October 2014, at 09:06. Although the genome of Xenopus tropicalis has been sequenced and published, other genomic tools and resources are still needed. An overview of CRISPR-Cas and TALEN genome editing advances in Xenopus laevis and Xenopus tropicalis that have the potential to revolutionize this classical model system.. See /XENLA_SA09023 for more details. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human … This page has been accessed 550,953 times. The Xenopus Gene Collection (XGC) is an NIH initiative that supports the production of cDNA libraries, clones and 5'/3' sequences to provide a set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis.All resources generated by the XGC are publicly accessible to the biomedical research community. In March of 2002 the Joint Genome Institute convened a meeting at the Production Genomics Facility in Walnut Creek, California. (2016) have sequenced the genome of another species, Xenopus laevis. The Xenopus laevis genome encodes a frog whose cells and body size are larger than those with smaller genomes. Xenopus Genome Project. Injection of base editor 3 (BE3) ribonucleoprotein targeting the tyrosinase (tyr) gene in early embryos can induce site-specific base conversions with the rates of up to 20.5%, resulting in oculocutaneous albinism phenotypes without … X. laevis is a model species so the genome should definite… Both species are fully aquatic, and are easy to maintain in captivity. X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data, X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data, Given that we currently see better mapping of the shotgun SA09023 reads to. As a group, amphibians are phylogenetically well positioned for comparisons to other vertebrates, having diverged from the amniote lineage (mammals, birds, reptiles) some 360 million years ago. X. tropicalis is also diploid (i.e., it has two sets of chromosomes), while X. laevis is allotetraploid (a form of tetraploid, i.e. 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. We suggest using a current version of, Wheeler & Brändli 2009 Dev Dyn 238:1287-1308, High-throughput multiwell-format screening, embryos tolerate extensive manipulation (e.g. Xenopus laevis genome has been only recently sequenced fully. A small, fast‐breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics.X. The Xenopus Gene Collection (XGC) is an NIH initiative that supports the production of cDNA libraries, clones and 5'/3' sequences to provide a set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis.All resources generated by the XGC are publicly accessible to the biomedical … To achieve this feat, the research team took advantage of new chromatin-related sequencing technologies as well as detailed microscopic examination of chromosomes with fluorescent markers. The frog's ventral surface is solid yellowish white to spotted. They may use data in publications focused around individual genes. RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. The frogs are then rested for a few months, when they can be induced again. In particular, seamlessly combining data from two species, Xenopus laevis —a tetraploid, and Xenopus tropicalis —a diploid ( 2), in an integrated environment is complex. Advantages of Xenopus as a Model Organism The earliest event in Xenopus development is the dorsal accumu-lation of nuclear β-catenin under the influence of cytoplasmic de-terminants displaced by fertilization. Initially, at the beginning of the 2000s, the tetraploid genome was thought to bring about problems that would not be observed if the diploid Xenopus tropicalis was chosen for sequencing. ), zebrafish (Danio rerio) , chicken (Gallus Gallus) and mice (Mus musculus) are used to discover the molecular mechanisms fundamental to life, thereby providing a shortcut to understanding human biology. See Xenopus_Genome_Project_Consortium page for the members & contributors of the project. A small, fast‐breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics.X. I converted original scaffold name to prevent confusion in comparison between different versions of the draft genome, because 'Scaffold102974' at XenBase/JGI 6.1 genome is different to 'Scaffold102974' at XenBase/JGI 7.2 genome. The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. In the last few years, numerous reports have demonstrated that TALENs are able to induce mutations in F0 Xenopus embryos, but none has demonstrated germline transmission of such mutations in X. laevis. However, little is known about the consequences of this duplication at the level of the genome… Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Xenbase hosts the full details and release information regarding the current Xenopus laevis genome . Mutations in the hsp4 gene in Xenopus results in lower pigmentation in the eyes and skin. Frog eggs are large (~1.2mm diameter), produced in large quantities, and easy to manipulate. 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. Global and overview maps 01100 Metabolic pathways 01200 Carbon metabolism 01210 2-Oxocarboxylic acid metabolism 01212 Fatty acid metabolism So in summary, Xenopus is a valuable tool because they are: Read more aboutBiological Discoveries and Biomedical Research using Xenopus (coming soon). Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. Description. If you have any question about this data in general, please contact Taejoon Kwon. 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