husbandry, cell biology, imaging, genetics, transgenesis, genomics). In the 1930's, doctors used Xenopus as a simple pregnancy test for women- because this hormone is present in the urine of a pregnant woman, the frog would be induced to lay eggs. 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. The high-quality draft sequence of the genome of X. tropicalis, often called the Western clawed frog, will also aid researchers who now use the frog’s more popular cousin, Xenopus laevis (zen’-uh-pus lay’-uh-vus), to study embryo development and cell biology. Global and overview maps 01100 Metabolic pathways 01200 Carbon metabolism 01210 2-Oxocarboxylic acid metabolism 01212 Fatty acid metabolism Xenopus laevis is an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011) for review). So in summary, Xenopus is a valuable tool because they are: Read more aboutBiological Discoveries and Biomedical Research using Xenopus (coming soon). In particular, seamlessly combining data from two species, Xenopus laevis —a tetraploid, and Xenopus tropicalis —a diploid ( 2), in an integrated environment is complex. Here we present a draft genome sequence assembly of X. tropicalis . 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. See Xenopus_Genome_Project_Consortium page for the members & contributors of the project. 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. Description. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. Data users may use data to analyze their own data, i.e. 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. For example, I renamed 'Scaffold102974' in XenBase/JGI 7.1 genome to 'JGIv7b.000102974'. 1. Sperm contribute genetic and epigenetic information to the embryo. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … Session et al. in X. laevis is active, or whether both contribute to different elements of gene expression. tropicalis shares advantages of X. laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic … 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. it has four sets of chromosomes), thus X.tropicalis is a more simple model for genetic studies. As soon as the paper is accepted, we will post that info on this website. The divergence time, in millions of years (Mya), is based on multiple gene divergence and protein divergence studies.Adapted from Wheeler & Brändli 2009 Dev Dyn 238:1287-1308. See XENLA_Genome page for detailed information about each version. Very few species of frog can be induced to produce eggs in such a controlled manner, and this is another reason why Xenopus is so popular with developmental and cell biologists. X. tropicalis is also diploid (i.e., it has two sets of chromosomes), while X. laevis is allotetraploid (a form of tetraploid, i.e. Xenopus laevis (African clawed frog) ... Genome annotation databases. 90% Identity; 50% Identity; Cross-references i … Advantages of Xenopus as a Model Organism 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. Molecular cloning of X. laevis urocortins. Major funding for Xenbase is provided by grant P41 HD064556. 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. If you have any question about this data in general, please contact Taejoon Kwon. X. laevis is a model species so the genome should definite… Although the genome of Xenopus tropicalis has been sequenced and published, other genomic tools and resources are still needed. Female X. laevis laevis are larger than males and average 110 mm in length (Kobel et al., 1996). The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' published the paper. The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. We show that during this period, DNA replication proceeds in an atypical manner. RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Genome Duplication Natural And Artificial Polyploidy (2n, 3n, 4n, 5n, 8n, 12n) The Xenopus genus includes various tetra-, octo- and dodecaploid species (Table 4) that were generated times over a period ranging from 80 to 10 millions years ago by interspecies hybridization through allopolyploidization (Evans et … Mutations in the hsp4 gene in Xenopus results in lower pigmentation in the eyes and skin. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. single cell , germ layer dissections, tissue transplantations, easy to inject of a range of materials (e.g. However, little is known about the consequences of this duplication at the level of the genome… This page was last modified on 14 October 2014, at 09:06. Each model organism has it's advantages and disadvantages, and these are compared in the table to the right (adapted from Wheeler and Brändli 2009). We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. "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). 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. There is a wealth of data in the literature on gene function, full-length cDNA sequences and in situ databases on laevis, but no genome sequence or genetics. The frogs are then rested for a few months, when they can be induced again. Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. Both species are fully aquatic, and are easy to maintain in captivity. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. 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. Periodic albino mutant X. laevis may be a useful model in studying this human syndrome. The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. The frog's ventral surface is solid yellowish white to spotted. The complete sequence of the 17,553-nucleotide Xenopus laevis mitochondrial genome has been determined. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. They display remarkable structural similarity with the human genome (Hellsten et al. nucleic acids, proteins, whole nuclei) into whole embryo or specific cells, cell fate of each early embryonic cell is known, allowing targeted gene knock-out, knockdown and overexpression studies, eggs and embryos provide abundant source for high-throughput biochemical studies, cell-free extracts made from Xenopus oocytes are a premier in vitro system for studies of fundamental aspects of cell and molecular biology, Xenopus oocytes are a leading system for studies of ion transport and channel physiology, Xenopus oocytes widely used assay environmental toxicology, large-scale genetic screens has identified genes involved in diverse developmental and physiological processes, hardy, fully aquatic and easy to maintain in the laboratory, eggs are a reliable and flexible material for research, embryos are a good model for vertebrate development, genetically similar to humans thus a good model for human disease. 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. Xenbase hosts the full details and release information regarding the current Xenopus laevis genome . 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. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human … (2016) have sequenced the genome of Xenopus laevis. Xenopus laevis genome has been only recently sequenced fully. 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 (GenBank accession no. (2016) have sequenced the genome of another species, Xenopus laevis. 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. Biologists utilize this same method to induce the production of eggs on demand in the laboratory. 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. The project rapidly expanded to include de novo reconstruction of X. laevis transcripts, in collaboration with groups around the world donating Illumina Hi-Seq RNA sequencing datasets, coordinating these efforts with genome sequencing by the Harland and Rokhsar groups at UC Berkeley and with Taira and collaborators at the University of Tokyo, Japan. 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. Data users may freely download and analyze data. 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. 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. Applications for the maternal host transfer technique combined with genome editing; Gene targeting and homology-directed repair; Circumventing lethal phenotypes; Xenopus genetics and husbandry issues arising in the creation of mutant lines; Both laevis and tropicalis will be used 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. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of con- Read More... Epigenetic sperm programming. 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. The NXR is funded by an award from the … Xenopus laevis (African clawed frog) Genome info Pathway map Brite hierarchy Module Genome map Blast Taxonomy: Search genes: KEGG pathway maps Metabolism. We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. The genomes of both X. laevis and X. tropicalis have been sequenced. 90% Identity; 50% Identity; Cross-references i … The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Egg production can be stimulated by injection of chorionic gonadotropin. 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. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 … 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. The Wallingford and Marcotte labs obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D), in conjunction with projects funded by the National Institutes of Health, to begin sequencing of the X. laevis genome. Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. 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