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. Fortunately, a closely related frog, Xenopus tropicalis, has a more amenable diploid genome and it also retains the same advantages as Xenopus laevis. 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. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. See XENLA_Genome page for detailed information about each version. 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 complete sequence of the 17,553-nucleotide Xenopus laevis mitochondrial genome has been determined. Xenopus laevisis an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011)for review). 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. 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 database for MS/MS proteomics data, and/or RNA-seq data. 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. As pets. The Xenopus laevis genome encodes a frog whose cells and body size are larger than those with smaller genomes. 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. The Xenopus model includes fully sequenced and annotated genomes of two species, X. tropicalis [8] and X. laevis [9], as well as large gene expression databases (all accessible through Xenbase - http://www.xenbase.org/common/). Both species are fully aquatic, and are easy to maintain in captivity. 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 … We began the project with Scott Hunicke-Smith at the University of Texas Genome Sequencing and Analysis facility, with funding sufficient for ~20x coverage of the X. laevis genome using ABI SOLiD next-generation sequencing. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. 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. Sperm contribute genetic and epigenetic information to the embryo. 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. The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' published the paper. 90% Identity; 50% Identity; Cross-references i … ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. Rapid embryo growth and development means that within a couple of days, a tadpole has a fully functional set of organs, and it can be examined to determine if any experimental intervention has had an effect. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. Although the genome of Xenopus tropicalis has been sequenced and published, other genomic tools and resources are still needed. single cell , germ layer dissections, tissue transplantations, easy to inject of a range of materials (e.g. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. Xenopus laevis (African clawed frog) Genome info Pathway map Brite hierarchy Module Genome map Blast Taxonomy: Search genes: KEGG pathway maps Metabolism. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. Data users may use data to analyze their own data, i.e. This makes them a valuable tool to investigate the early period of embryonic development. The genomes of both X. laevis and X. tropicalis have been sequenced. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … 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. The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. 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. 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 frog's ventral surface is solid yellowish white to spotted. In addition to the key attributes of these embryos for in vivoimaging, cell-free extracts from Xenopusprovide among the most powerful in vitrosystems for studies of cell and molecular biology. Xenopus laevis laevis has a yellowish to darker, spotted to marbled dorsal coloring. 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. 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. RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Advantages of Xenopus as a Model Organism 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. 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. 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. 90% Identity; 50% Identity; Cross-references i … Frog eggs are large (~1.2mm diameter), produced in large quantities, and easy to manipulate. From Marcotte Lab. So in summary, Xenopus is a valuable tool because they are: Read more aboutBiological Discoveries and Biomedical Research using Xenopus (coming soon). Jump to: navigation, search. 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. Here we present a draft genome sequence assembly of X. tropicalis . 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 … GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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. Genome evolution in the allotetraploid frog Xenopus laevis. (a) Schematic representation of Xenopus laevis genes in chromosome 1L containing hps4 locus and in chromosome 1S (v9.2, Xenbase). Here we present a draft genome sequence assembly of X. tropicalis . Female X. laevis laevis are larger than males and average 110 mm in length (Kobel et al., 1996). 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. Major funding for Xenbase is provided by grant P41 HD064556. "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). 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. Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. 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 current version is named 'JGI 7.1' at XenBase, and 'JGIv7b' at UTA web repository('daudin'). Xenbase: The Xenopus Model Organism Knowledgebase. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Hello! Xenopus_laevis_v2 Organism: Xenopus laevis (African clawed frog) Submitter: International Xenopus Sequencing Consortium Date: 2016/08/09 Assembly level: Chromosome Genome representation: full RefSeq category: representative genome Synonyms: xenLae2 GenBank assembly accession: GCA_001663975.1 (latest) RefSeq assembly accession: GCF_001663975.1 (latest) IDs: 779791[UID] 337849… Few studies have successfully used CRISPR in … Availability of X. laevis genome sequence makes this allotetraploid species amenable to genome editing.. Genome editing in this system offers unique opportunities for modeling human disease. The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. 1. The frogs are then rested for a few months, when they can be induced again. Data users may freely download and analyze data. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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. Read More... Epigenetic sperm programming. Biologists utilize this same method to induce the production of eggs on demand in the laboratory. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human … A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. 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. Two species of Xenopus are regularly used by biologists, Xenopus laevis and Xenopus tropicalis. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. 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. See /XENLA_SA09023 for more details. 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 … 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. Xenopus laevis (African clawed frog) ... Genome annotation databases. 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. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. They may use data in publications focused around individual genes. Because X. tropicalis is diploid and the X. laevis is tetraploid, important inferences can be made about genome evolution. The NXR is funded by an award from the … 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. Xenopus laevis genome has been only recently sequenced fully. Periodic albino mutant X. laevis may be a useful model in studying this human syndrome. 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 During Xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. 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. 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. 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. 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. in X. laevis is active, or whether both contribute to different elements of gene expression. Completion of the Xenopus laevis genome sequence from inbred J strain animals has facilitated the generation of germline mutant X. laevis using targeted genome editing. Session et al. As soon as the paper is accepted, we will post that info on this website. Description. Three mate paired libraries were sequenced: This (very roughly) corresponds to >600X coverage by raw data, ~50X coverage by high quality data, of the BAC set. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. When the Joint Genome Institute decided to sequence a frog genome, however, the Xenopus research community recommended X. tropicalis over X. laevis because tropicalis has half the genome size. 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