Status
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. 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.
Collaborators
- Richard Harland , University of California at Berkeley
- Rob Grainger , University of Virginia
Genome Reference(s)
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS
The genome of the Western clawed frog Xenopus tropicalis.
Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670
Links
- Useful links and articles:Xenopus express
- Frog genetics: Xenopus tropicalis leaps into the future
- Trans-NIH Xenopus initiative