Xenopus tropicalis v4.1
 
Project Status

The genome of Xenopus (Silurana) tropicalis is estimated to be approximately 1.7 billion base pairs contained in 10 pairs of chromosomes, and is being sequenced to approximately 8X depth.

The genome assembly release v4.1 was annotated using the JGI annotation pipeline. Gene models and associated transcripts/proteins are predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. The current release contains approximately 28,000 gene models composed of known X. tropicalis genes as well as support from available X. tropicalis and X. laevis EST and cDNA data.

Approximately 95% of X. tropicalis full-length cDNAs mapped to the V 4.1 assembly. Average gene length is 16.5 kb and average transcript length is 1.3kb, with the average protein containing 409 amino acids. There are approximately 6.5 exons per gene averaging 200bp each with intron spacing of 2.8kb. Gene functions have been automatically assigned based on homology to known genes. Manual curation of these annotations is ongoing.

 
Assembly Releases

v.4.1 (August 2005): The reads were asembled using JAZZ, the JGI assembler producing a genome of approximately 1.5 Gb. The assembly contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half of the genome is contained in 272 scaffolds, all at least 1.56 Mb in length. Some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed and placed in a separate directory (more information is available here). The genome will be improved over the coming year by additional sequencing of large insert clones, targeted gap closure, and incorporation of physical and genetic mapping information as it becomes available.

v.4.0 (June 2005): The assembly release version 4.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.65X. After trimming for vector and quality, 22.5 Million reads assembled into 19,759 scaffolds totaling 1.51 Gbp. Roughly half of the genome is contained in 272 scaffolds all at least 1.56 Mb in length.

v.3.0 (October 2004): The assembly release version 3.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 Million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half of the genome is contained in 392 scaffolds all at least 1.2 Mb in length.

 
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Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.