A HIGH QUALITY GENOME ASSEMBLY FOR XENOPUS TROPICALIS
Soleyman Daniel
University Of California Berkeleycity: Berkeley country: United States (us)
Grant 5R01GM086321-04 from National Institute Of General Medical Sciences
Keywords: Adopted; Age; Animal Model; Animals; Annotation, Automated; base; Biochemical; Biological; Bypass; Cataloging; Catalogs; Cell Proliferation; Cells; Chromosome Mapping; Chromosome Structures; Chromosomes; Cloning; Communities; Complement; computerized data processing; Data; Databases; density; Department of Energy; Development; Developmental Cell Biology; DNA; DNA Sequence; egg; Embryo; Ensure; Europe; Event; Evolution; Expressed Sequence Tags; Family; Female; Frequencies (time pattern); gene function; Genes; Genome; Genomics; Haploidy; Health; Human; Human Development; human disease; Human Genome; Hybrids; improved; insight; Institutes; Ivory Coast; Joints; Libraries; Life; Maintenance; Mammals; Maps; Methods; Microinjections; Microsurgery; Mothers; Physical Chromosome Mapping; Polymerase Chain Reaction; Process; Property; Proteome; Proteomics; Radiation Hybrid; Research; Resources; scaffold; Sequence Analysis; sex; Shotgun Sequencing; simple sequence length polymorphism; Single Nucleotide Polymorphism; Source; Structure; Systems Biology; Time; Universities; Vertebrates; Washington; Work; Xenopus; xenopus genome
Project start date: 2009-01-01
Project end date: 2012-12-31
Budget start date: 1-JAN-2012
Budget end date: 31-DEC-2012
5R01GM086321-04 (2012): $245714
Sponsored Links Excellgen http://Excellgen.com
Grants awarded to Soleyman Daniel
A GENOME ASSEMBLY FOR XENOPUS LAEVIS
Soleyman Daniel
University Of California Berkeleycity: Berkeley country: United States (us)
Grant 5R01HD065705-02 from Eunice Kennedy Shriver National Institute Of Child Health & Human Development
Abstract: Research on the amphibian Xenopus has provided numerous new insights into cell and developmental biology. With their large size and abundance, they provide unparalleled material for biochemical and cell biological analysis of complex processes such as the cell cycle and chromosome mechanics. For embryological experiments, the embryos are readily manipulated by microsurgery and by microinjection can be subjected to gain or loss of gene function. In order to make Xenopus more useful for the modern age of "systems biology" where proteomic and genomic analyses promise a comprehensive understanding of life´s processes, we propose here to complement the genome assembly of Xenopus tropicalis with a gene and protein level genome assembly for Xenopus laevis. The allotetraploid Xenopus laevis is in wider use than the smaller, diploid Xenopus tropicalis, because of its history, robustness, and the size and quantity of eggs that can be obtained for embryological and cell biological experiments. We propose to carry out high throughput sequencing of X. laevis, and generate a gene-scale assembly. By selecting regions complementary to the X. tropicalis sequence we will be able to assemble X. laevis genes from relatively inexpensive, short read data. The project provides some computational challenges that will need to be overcome and the approaches developed will be of wide utility in characterizing genomes of other organisms. We will provide support for genome annotation by Xenbase and deposit gene and protein collections in public databases to ensure that the resources are widely available. Xenopus laevis eggs and embryos have been the material of choice for work on vertebrate experimental embryology and biochemical dissection of the cell cycle, providing insights into human biology. We propose to fill a large gap in the essential resources for this work, namely a catalogue of the gene and protein content
Keywords: African; Age; Algorithms; Amphibia; Antisense Oligonucleotides; Biochemical; Biochemistry; Biological; Biological Models; blastomere structure; Cataloging; Catalogs; Cell Cycle; Cells; Cellular biology; Chromosomes; Code; Collaborations; Collection; Communities; comparative genomics; Complement; Complex; Computing Methodologies; Data; Data Set; Databases; Department of Energy; Deposition; design; Development; Developmental Cell Biology; Diploidy; Dissection; DNA Sequence; egg; Embryo; Embryology; Embryonic Development; Ensure; Evolution; Functional RNA; Gene Expression Profile; gene function; Gene Proteins; Genes; Genetic; Genome; genome sequencing; Genomics; Human Biology; improved; insight; Institutes; Joints; Libraries; Life; Mammals; Mechanics; Microinjections; Microsurgery; Organism; Ovum; paralogous gene; Peptides; Process; Proteome; Proteomics; public health relevance; Reading; Reagent; Recording of previous events; Relative (related person); Research; research study; Resources; RNA; RNA Splicing; Systems Biology; Technology; transcriptomics; Validation; Work; Xenopus; Xenopus laevis; Xenopus sp
Relevance: Relevance Xenopus laevis eggs and embryos have been the material of choice for work on vertebrate experimental embryology and biochemical dissection of the cell cycle, providing insights into human biology. We propose to fill a large gap in the essential resources for this work, namely a catalogue of the gene and protein content
Project start date: 2010-08-01
Project end date: 2014-05-31
Budget start date: 1-JUN-2011
Budget end date: 31-MAY-2012
PFA/PA: PAR-09-240
5R01HD065705-02 (2011): $305772