The Xenopus ORFeome: A resource that enables functional genomics

Area of Science:

• * Developmental Biology
• * Genomics
• * Molecular Biology

Background:

• * Functional characterization of proteins and systems-level studies require accessible sets of cloned open reading frames (ORFs).
• * The Xenopus laevis model organism is crucial for understanding vertebrate development and gene function.
• * Existing resources for Xenopus laevis gene expression and function are being expanded.

Purpose of the Study:

• * To release the first stage of the Xenopus ORFeome, comprising 8673 ORFs from the Xenopus Gene Collection (XGC).
• * To enable rapid in-frame transfer of ORFs into expression vectors using the Gateway® system.
• * To provide a valuable resource for functional genomics and disease modeling in Xenopus.

Main Methods:

• * Cloned 8673 ORFs from the Xenopus Gene Collection (XGC) into a Gateway® donor vector.
• * Validated Gateway® system transfer via 5' and 3' end sequencing of the entire ORF collection.
• * Re-analyzed ORF predictions to verify quality and identify potential truncations.

Main Results:

• * Released 8673 ORFs, representing approximately 40% of the non-redundant Xenopus laevis gene complement (estimated 7871 unique genes).
• * Identified 2724 ORFs with human orthologs associated with disease.
• * Integrated data into Xenbase, linking ORFs with genomic, expression, function, and human disease metadata.

Conclusions:

• * The Xenopus ORFeome V1.0 is a significant resource for the research community, enabling large-scale functional studies.
• * This collection facilitates the use of Xenopus as a model for human disease research.
• * The integrated data and commercial availability enhance the utility of the ORFeome for diverse applications.