Xenopus Finishing

Xenopus tropicalis (the pipid frog) is an ideal vertebrate model system for developmental biology. The species has several advantages over other Xenopus species including it being diploid, having a relatively small genome size (1.7Gb and 10 chromosome pairs) and a short, four-six month, generation time.

The Xenopus tropicalis genome is currently being sequenced at the Joint Genome Institute (JGI) in Walnut Creek, CA. Using a whole genome shotgun approach (WGS) 3kb and 8kb shotgun have been generated and are being sequenced. Versions of the whole genome assembly will be released at regular intervals as data accumulates, with a final draft assembly based on ~8X sequence estimated to be completed in the first half of 2005.

In collaboration with the JGI and funding from the Department of Energy, the Stanford Human Genome Center is finishing Xenopus tropicalis clones from 2 BAC libraries. After the selection of large insert clones for sequencing, shotgun libraries are produced at the JGI and the clones drafted to an average depth of 10x. Shotgun data, subclone libraries and the large insert glycerol stock are then transferred to the SHGC, where the draft data is finished to meet our high quality standards.

We are finishing Xenopus tropicalis BACs from two main areas:
1. BACs containing genes of interest suggested by the community
2. BACs containing regions syntenic to 30Mb segment of the human genome selected as part of the ENCODE project.