Genome reannotation of the African clawed frog Xenopus laevis for gene expression studies

Project: Research project

Project Details

Description

Genome reannotation of the African clawed frog Xenopus laevis for gene expression studies Genome reannotation of the African clawed frog, Xenopus laevis, for gene expression studies Work to Be Performed: 1. For genome reannotation, we will use the integrated genome assembly builds from the Joint Genome Institute (USA) and the National Institute of Genetics (Japan), and we will confer with these institutions and the Xenbase community portal to ensure that the annotation will be based on a stable genome build. 2. Transcript sequences for genome reannotation will combined publicly deposited data (EST Sanger-based sequences and next-gen RNA-Seq data) combined with unpublished RNA-Seq data generated by Kendall Jensen at TGen deriving from RNAs collected from tissues by the laboratory of Holly Cline at the Scripps Institute. We will continue to monitor for newly deposited data that would improve the genome reannotation. 3. De novo transcriptome assembly will be carried out using Trinity (Grabherr et al., 2011). Then, these assembled contigs will be aligned to the Xenopus laevis genome build (above) using the gmap tool within PASA, with the aim of i) eliminating sequences not aligning to the genome and ii) merging de novo assembled sequences to remove redundancy. 4. After consultation with Dr. Kendall Jensen, we will regularly confer and share annotations files for the research community. This includes Xenbase, a resource for the Xenopus research community, as well as the major international genome portals Ensembl (European Bioinformatics Institute), the University of California Santa Cruz Genome Browser (UCSC), and the National Institute of Health National Center for Biotechnology Information (NCBI). 5. RNA-Seq analysis: Our group has demonstrated expertise in RNA-Seq analysis of gene expression levels (Eckalbar et al., 2012; Hutchins et al., in review). We will share our expertise and be available to consult with Dr. Holly Cline for RNA-Seq analysis in the Xenopus model system.
StatusFinished
Effective start/end date5/1/1410/31/16

Funding

  • Translational Genomics Research Institute (TGen): $45,000.00

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