(2016) have sequenced the genome of another species, Xenopus laevis. 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 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. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. 90% Identity; 50% Identity; Cross-references i … 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. Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. "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). 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. We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. Xenbase: The Xenopus Model Organism Knowledgebase. Major funding for Xenbase is provided by grant P41 HD064556. 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. husbandry, cell biology, imaging, genetics, transgenesis, genomics). The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. We're posting our intermediate datasets here in advance of publication for use by the wider community. 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. reference database for MS/MS proteomics data, and/or RNA-seq data. 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 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 is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Few studies have successfully used CRISPR in … Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. Xenopus laevisis an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011)for review). About the XGC. Xenopus laevis genome has been only recently sequenced fully. 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. 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 … 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. As pets. Session et al. We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. ), 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. 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. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. 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. 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 … Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. For example, I renamed 'Scaffold102974' in XenBase/JGI 7.1 genome to 'JGIv7b.000102974'. As soon as the paper is accepted, we will post that info on this website. Description. X. tropicalis is also diploid (i.e., it has two sets of chromosomes), while X. laevis is allotetraploid (a form of tetraploid, i.e. 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. Molecular cloning of X. laevis urocortins. Xenbase hosts the full details and release information regarding the current Xenopus laevis genome . 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. 90% Identity; 50% Identity; Cross-references i … 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. Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. The current version is named 'JGI 7.1' at XenBase, and 'JGIv7b' at UTA web repository('daudin'). 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. 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 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. 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- The frog's ventral surface is solid yellowish white to spotted. 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 (African clawed frog) ... Genome annotation databases. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. 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. This page has been accessed 550,953 times. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. 90% Identity; 50% Identity; Cross-references i … From Marcotte Lab. Sperm contribute genetic and epigenetic information to the embryo. 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. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. Because X. tropicalis is diploid and the X. laevis is tetraploid, important inferences can be made about genome evolution. 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. Genomes were aligned using Synteny Mapping and Analysis Program (SyMAP) v 4.2 [ … 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 complete sequence of the 17,553-nucleotide Xenopus laevis mitochondrial genome has been determined. This makes them a valuable tool to investigate the early period of embryonic development. However, little is known about the consequences of this duplication at the level of the genome… Read More... Epigenetic sperm programming. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. Xenopus laevis (African clawed frog) ... Genome annotation databases. Session et al. 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. Female X. laevis laevis are larger than males and average 110 mm in length (Kobel et al., 1996). Gene expression knockdown techniques Biologists utilize this same method to induce the production of eggs on demand in the laboratory. Frog embryos develop externally, allowing experiments to be performed prior to, or directly following fertilization. The frog Xenopus laevis has been an important model of vertebrate cell biology and development for many decades. (2016) have sequenced the genome of Xenopus laevis. The frogs are then rested for a few months, when they can be induced again. 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 GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. This subspecies has a fifth toe that is much longer than the tibia. The genomes of both X. laevis and X. tropicalis have been sequenced. 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. Frog eggs are large (~1.2mm diameter), produced in large quantities, and easy to manipulate. In March of 2002 the Joint Genome Institute convened a meeting at the Production Genomics Facility in Walnut Creek, California. Xenopus laevis is an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011) for review). Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. About the XGC. Advantages of Xenopus as a Model Organism 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. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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. (a) Schematic representation of Xenopus laevis genes in chromosome 1L containing hps4 locus and in chromosome 1S (v9.2, Xenbase). See /XENLA_SA09023 for more details. 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. 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. 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 … 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. single cell , germ layer dissections, tissue transplantations, easy to inject of a range of materials (e.g. 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. 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. The main difference between the XenBase/JGI genome and UTA genome is the scaffold name. 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. Fortunately, a closely related frog, Xenopus tropicalis, has a more amenable diploid genome and it also retains the same advantages as Xenopus laevis. 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 … Xenopus laevis (v9.1 genome assembly) L sub-genome, and (iii) XLA.S: X. laevis S sub-genome. Two species of Xenopus are regularly used by biologists, Xenopus laevis and Xenopus tropicalis. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. X. The hps4 gene is present only in chromosome 1L, and a 1.9 kb genomic deletion including two exons in the hps4.L gene occurs in the periodic albino mutant. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. 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. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. 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. During Xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. Several features make Xenopus eggs and embryos an outstanding tool in biomedical research. 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. Hello! They may use data in publications focused around individual genes. Mutations in the hsp4 gene in Xenopus results in lower pigmentation in the eyes and skin. 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.. Here we present a draft genome sequence assembly of X. tropicalis . Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. 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… 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. 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. 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. 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. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early 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. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. Xenopus laevis (African clawed frog) ... Genome annotation databases. X. laevis is a model species so the genome should definite… 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. Global and overview maps 01100 Metabolic pathways 01200 Carbon metabolism 01210 2-Oxocarboxylic acid metabolism 01212 Fatty acid metabolism Phylogenetic tree showing the main animal models commonly used in biomedical research and their evolutionary relationships. Alternatively, you can download them at UTA 'daudin' web repository. 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 … 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. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … 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. 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