Implications for Xenopus genomics

Because Xenopus laevis is an important model system for developmental biology and aquatic toxicology, it has been suggested that a full-scale genomic sequencing effort should be undertaken, i.e., a Xenopus Genome Project. As indicated above, this would be a complex undertaking for a variety of reasons, including the variability among individual frogs of this noninbred strain, the possibility of allelic variants for most expressed genes, etc. Silurana has been suggested as a potential substitute species since it appears to be a closely related diploid; other experimental factors, such as egg clutch size, time to sexual maturity, etc., make it more useful than Xenopus for some types of experiments.8 Still, there is variability among Silurana transcripts as well, that perhaps can be accounted for by individual polymorphisms but may also indicate nondiploidy. It seems likely that a full-scale sequencing effort will be accomplished someday, for one or both organisms, but it also seems likely that this will be only after a large number of other diploid organisms, pathogenic microorganisms, and others have been sequenced to completion.

In the meantime, Xenopus ESTs are being sequenced at a high rate and improved tools for clustering sequences have led us to propose the Virtual Xenopus Genome Project. The goal of this project will be to condense the raw EST sequence traces into individual contigs that represent full-length transcripts for Xenopus expressed genes. Because of the likelihood that a high proportion of Xenopus genes will be represented by at least two alleles, it will be necessary to improve the resolution of currently available clustering tools so that individual alleles can be distinguished; these alleles can also be aligned with each other so that common and distinct regions are identified for use in microarray and other types of transcript analyses. A method should also be developed to identify and curate single nucleotide and other polymorphisms in the Xenopus EST sequences. The data from the EST collections should also be available for comparison and clustering with archival genomic and cDNA sequence data in GenBank for which individual sequence traces are not available. Such a data repository should be kept current by adding and updating contigs as new ESTs and other Xenopus sequences are added to GenBank. Because of the expected frequency of allelic variants and polymorphism, a significant amount of manual curation will be required to keep such a database current and to resolve database management issues such as establishing rules for the labeling of allelic variants, isotypes, and polymorphisms and developing a systematic nomenclature. However, we believe that such an undertaking will maximize the utility of the large Xenopus EST database, and the result might be a catalogue of all expressed Xenopus alleles and their common variants.

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