Here we present a draft genome sequence assembly of X. tropicalis . X. 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. 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. Global and overview maps 01100 Metabolic pathways 01200 Carbon metabolism 01210 2-Oxocarboxylic acid metabolism 01212 Fatty acid metabolism Color code: green, best in category; red, worst in category. ), 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. 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. Session et al. Here we present a draft genome sequence assembly of X. tropicalis . Data users may freely download and analyze data. Phylogenetic tree showing the main animal models commonly used in biomedical research and their evolutionary relationships. Xenopus laevis (African clawed frog) ... Genome annotation databases. Few studies have successfully used CRISPR in … The frogs are then rested for a few months, when they can be induced again. 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. 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. Hello! Major funding for Xenbase is provided by grant P41 HD064556. The comparison with mammalian and bird genomes also provides an opportunity to examine the dynamics of tetrapod chromosomal evolution. 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. 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). Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Alternatively, you can download them at UTA 'daudin' web repository. The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' published the paper. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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.. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. Sperm contribute genetic and epigenetic information to the embryo. Biologists utilize this same method to induce the production of eggs on demand in the laboratory. See Xenopus_Genome_Project_Consortium page for the members & contributors of the project. 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. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 … Molecular cloning of X. laevis urocortins. Because X. tropicalis is diploid and the X. laevis is tetraploid, important inferences can be made about genome evolution. Gene expression knockdown techniques During Xenopus laevis early development, the genome is replicated in less than 15 min every 30 min. 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. Jump to: navigation, search. Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. However, little is known about the consequences of this duplication at the level of the genome… Xenopus laevis have been kept as pets and research subjects since as early as the 1950s. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. This page was last modified on 14 October 2014, at 09:06. GeneID i: 398045: KEGG i: xla:398045 Similar proteins i. 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. Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. 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 From Marcotte Lab. 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. 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/). Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. 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 … reference database for MS/MS proteomics data, and/or RNA-seq data. They display remarkable structural similarity with the human genome (Hellsten et al. Xenopus Genome Project. Both species are fully aquatic, and are easy to maintain in captivity. In particular, seamlessly combining data from two species, Xenopus laevis —a tetraploid, and Xenopus tropicalis —a diploid ( 2), in an integrated environment is complex. Experimental organisms such as frogs (X. laevis and X. tropicalis), nematode worms (C. elegans), fruit flies (Drosphilia spp. 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. Xenopus laevis is an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011) for review). The genomes of both X. laevis and X. tropicalis have been sequenced. They display remarkable structural similarity with the human genome (Hellsten et al. Frog embryos develop externally, allowing experiments to be performed prior to, or directly following fertilization. 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). 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. 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. 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. 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! See /XENLA_SA09023 for more details. For example, I renamed 'Scaffold102974' in XenBase/JGI 7.1 genome to 'JGIv7b.000102974'. Several features make Xenopus eggs and embryos an outstanding tool in biomedical research. Mutations in the hsp4 gene in Xenopus results in lower pigmentation in the eyes and skin. 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 (African clawed frog) ... Genome annotation databases. (2016) have sequenced the genome of Xenopus laevis. 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. 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. 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 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. 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 … Female X. laevis laevis are larger than males and average 110 mm in length (Kobel et al., 1996). As pets. 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 Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. 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. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. 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. They may use data in publications focused around individual genes. ,2010) meaning that findings from Xenopus provide insights into many human conditions and diseases. it has four sets of chromosomes), thus X.tropicalis is a more simple model for genetic studies. XenOrtho DB (Xenopus Ortholog DataBase) is a database in which ortholog genes of Xenopus tropicalis, Xenopus laevis and humans are listed. 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. Frog eggs are large (~1.2mm diameter), produced in large quantities, and easy to manipulate. The frog's ventral surface is solid yellowish white to spotted. 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. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human … 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. 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. 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… Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. Biallelic genome modification in F 0 Xenopus tropicalis embryos using the CRISPR/Cas system Ira L. Blitz. 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 (African clawed frog) Genome info Pathway map Brite hierarchy Module Genome map Blast Taxonomy: Search genes: KEGG pathway maps Metabolism. "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). 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. About the XGC. 1. Genetic studies in this organism are not practical because of the tetraploid nature of the genome and the long generation time of … Genomes were aligned using Synteny Mapping and Analysis Program (SyMAP) v 4.2 [ … 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 Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Xenopus laevisis an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011)for review). The genomes of both X. laevis and X. tropicalis have been sequenced. (2016) have sequenced the genome of another species, Xenopus laevis. 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 frog Xenopus laevis has been an important model of vertebrate cell biology and development for many decades. 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. 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 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. Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. You can download X. laevis genomes at XenBase FTP site. (a) Schematic representation of Xenopus laevis genes in chromosome 1L containing hps4 locus and in chromosome 1S (v9.2, Xenbase). 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. GeneID i: 398006: KEGG i: xla:398006 Similar proteins i. husbandry, cell biology, imaging, genetics, transgenesis, genomics). 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. 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. Read More... Epigenetic sperm programming. 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. 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. The main difference between the XenBase/JGI genome and UTA genome is the scaffold name. 90% Identity; 50% Identity; Cross-references i … 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. Advantages of Xenopus as a Model Organism single cell , germ layer dissections, tissue transplantations, easy to inject of a range of materials (e.g. 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. 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. 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 … We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. Although the genome of Xenopus tropicalis has been sequenced and published, other genomic tools and resources are still needed. Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. 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 … 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. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis. See XENLA_Genome page for detailed information about each version. Two species of Xenopus are regularly used by biologists, Xenopus laevis and Xenopus tropicalis. Genome evolution in the allotetraploid frog 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. 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. Xenopus laevis (African clawed frog) ... Genome annotation databases. The Xenopus laevis genome is the first amphibian to have its genome sequence reported as complete chromosomes. Description. So in summary, Xenopus is a valuable tool because they are: Read more aboutBiological Discoveries and Biomedical Research using Xenopus (coming soon). Fortunately, a closely related frog, Xenopus tropicalis, has a more amenable diploid genome and it also retains the same advantages as Xenopus laevis. Official gene annotation/genome browser is served at XenBase. Despite the genomic revolution, the first complete genome of a frog, Xenopus tropicalis, was sequenced only in 2010. X. laevis is a model species so the genome should definite… This makes them a valuable tool to investigate the early period of embryonic development. 90% Identity; 50% Identity; Cross-references i … Data users may use data to analyze their own data, i.e. 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. 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 … Xenopus laevis genome has been only recently sequenced fully. 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… 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 African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. 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. The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. 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 comparison of this amphibian mitochondrial genomic sequence with those of the mammalian mitochondrial genomes reveals a similar gene order and compact genomic organization. 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 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. We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. If you have any question about this data in general, please contact Taejoon Kwon. We show that during this period, DNA replication proceeds in an atypical manner. 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. 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're posting our intermediate datasets here in advance of publication for use by the wider community. 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. 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