Xenopus is a premier system for studying early vertebrate developmental and cell biology. The availability of genomic sequence has enabled genomic and genetic analyses. However, annotation of gene models in the X. tropicalis genome remains poor, hampering these efforts. In this proposal, we will perform targeted sequencing to annotate the genic part of the genome. This will include 1) transcript sequencing to assemble the transcriptome and identify temporal gene expression, 2) sequence capture to fill gaps in the genic portions of the genome, and 3) SNP identification to facilitate genetics. Improved annotation of the genic portion of the X. tropicalis genome assembly will enable many priorities of the Xenopus community that are outlined in the 2009 Xenopus White Paper: 1) it will make a more complete ORFeome possible 2) greatly facilitate genetics and 3) improve the assembly of the X. laevis genome. For these reasons, the 2009 Xenopus Community White Paper lists "Improvement of the X. tropicalis genome sequence and annotation" as an essential resource.

Public Health Relevance

In order to better understand human health, we model human biology using frogs specially Xenopus. In this proposal, we will improve a critical resource for studying Xenopus, its genomic sequence, in order to better use this system to understand human biology and disease.

National Institute of Health (NIH)
Research Project (R01)
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Study Section
Special Emphasis Panel (ZRG1)
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Hoodbhoy, Tanya
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Yale University
Schools of Medicine
New Haven
United States
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Owens, Nick D L; Blitz, Ira L; Lane, Maura A et al. (2016) Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep 14:632-47
Forouzmand, Elmira; Owens, Nick D L; Blitz, Ira L et al. (2016) Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Dev Biol :
Abu-Daya, Anita; Khokha, Mustafa K; Zimmerman, Lyle B (2012) The hitchhiker's guide to Xenopus genetics. Genesis 50:164-75