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. This makes them a valuable tool to investigate the early period of embryonic development. GeneID i: 398045: KEGG i: xla:398045 Similar proteins i. For example, I renamed 'Scaffold102974' in XenBase/JGI 7.1 genome to 'JGIv7b.000102974'. We show that during this period, DNA replication proceeds in an atypical manner. 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. Xenopus laevis (African clawed frog) ... Genome annotation databases. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. Gene expression knockdown techniques 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. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human … 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 … 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. A comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. Alternatively, you can download them at UTA 'daudin' web repository. 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 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. As pets. 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 African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. Biologists utilize this same method to induce the production of eggs on demand in the laboratory. Xenbase hosts the full details and release information regarding the current Xenopus laevis genome . husbandry, cell biology, imaging, genetics, transgenesis, genomics). Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. Major funding for Xenbase is provided by grant P41 HD064556. 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. 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. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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. Xenopus is a genus of African frogs that are commonly known as the African clawed frogs. 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. 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 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. 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. The Xenopus laevis genome encodes a frog whose cells and body size are larger than those with smaller genomes. 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 … As soon as the paper is accepted, we will post that info on this website. 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.. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. If you have any question about this data in general, please contact Taejoon Kwon. 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. From Marcotte Lab. 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. So in summary, Xenopus is a valuable tool because they are: Read more aboutBiological Discoveries and Biomedical Research using Xenopus (coming soon). single cell , germ layer dissections, tissue transplantations, easy to inject of a range of materials (e.g. 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 … This page has been accessed 550,953 times. reference database for MS/MS proteomics data, and/or RNA-seq data. Xenbase: The Xenopus Model Organism Knowledgebase. Advantages of Xenopus as a Model Organism XenOrtho DB (Xenopus Ortholog DataBase) is a database in which ortholog genes of Xenopus tropicalis, Xenopus laevis and humans are listed. However, little is known about the consequences of this duplication at the level of the genome… 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). 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. Female X. laevis laevis are larger than males and average 110 mm in length (Kobel et al., 1996). GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. (2016) have sequenced the genome of 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 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. Fortunately, a closely related frog, Xenopus tropicalis, has a more amenable diploid genome and it also retains the same advantages as Xenopus laevis. The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. 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. 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… "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 NXR is funded by an award from the … Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. 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 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. 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. Xenopus laevis (African clawed frog) ... Genome annotation databases. 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… 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. 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. Experimental organisms such as frogs (X. laevis and X. tropicalis), nematode worms (C. elegans), fruit flies (Drosphilia spp. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. The main difference between the XenBase/JGI genome and UTA genome is the scaffold name. Here we present a draft genome sequence assembly of X. tropicalis . 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 … The complete sequence of the 17,553-nucleotide Xenopus laevis mitochondrial genome has been determined. Because X. tropicalis is diploid and X. laevis is tetraploid, important inferences can be made about genome evolution. Both species are fully aquatic, and are easy to maintain in captivity. 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 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 genomes of both X. laevis and X. tropicalis have been sequenced. 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. Xenopus laevis is an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011) for review). Hello! The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. You can download X. laevis genomes at XenBase FTP site. Color code: green, best in category; red, worst in category. 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 Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Periodic albino mutant X. laevis may be a useful model in studying this human syndrome. See XENLA_Genome page for detailed information about each version. 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. 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. This subspecies has a fifth toe that is much longer than the tibia. 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 frog's ventral surface is solid yellowish white to spotted. Because X. tropicalis is diploid and the X. laevis is tetraploid, important inferences can be made about genome evolution. 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 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/). Molecular cloning of X. laevis urocortins. Genomes were aligned using Synteny Mapping and Analysis Program (SyMAP) v 4.2 [ … Xenopus laevis laevis has a yellowish to darker, spotted to marbled dorsal coloring. The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. 1. See /XENLA_SA09023 for more details. 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 publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' published the paper. 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. About the XGC. Jump to: navigation, search. Here we present a draft genome sequence assembly of X. tropicalis . 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. Session et al. 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 Genome Project. 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. This page was last modified on 14 October 2014, at 09:06. 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. Read More... Epigenetic sperm programming. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. Two species of Xenopus are regularly used by biologists, Xenopus laevis and Xenopus tropicalis. Official gene annotation/genome browser is served at XenBase. In March of 2002 the Joint Genome Institute convened a meeting at the Production Genomics Facility in Walnut Creek, California. 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. Frog eggs are large (~1.2mm diameter), produced in large quantities, and easy to manipulate. See Xenopus_Genome_Project_Consortium page for the members & contributors of the project. We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. 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. Sperm contribute genetic and epigenetic information to the embryo. The current version is named 'JGI 7.1' at XenBase, and 'JGIv7b' at UTA web repository('daudin'). 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 Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … Description. 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). 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. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. Phylogenetic tree showing the main animal models commonly used in biomedical research and their evolutionary relationships. During Xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. 90% Identity; 50% Identity; Cross-references i … They display remarkable structural similarity with the human genome (Hellsten et al. X. laevis is a model species so the genome should definite… Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. (2016) have sequenced the genome of another species, Xenopus laevis. We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. We're posting our intermediate datasets here in advance of publication for use by the wider community. 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. 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 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. X. tropicalis is also diploid (i.e., it has two sets of chromosomes), while X. laevis is allotetraploid (a form of tetraploid, i.e. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. Global and overview maps 01100 Metabolic pathways 01200 Carbon metabolism 01210 2-Oxocarboxylic acid metabolism 01212 Fatty acid metabolism Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. Xenopus laevis (African clawed frog) Genome info Pathway map Brite hierarchy Module Genome map Blast Taxonomy: Search genes: KEGG pathway maps Metabolism. The frogs are then rested for a few months, when they can be induced again. Session et al. 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. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. 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. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. Data users may freely download and analyze 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. Xenopus laevisis an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011)for review). The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. 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. 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