Info • Volvox carteri nagariensis
The data on this Volvox portal is for archival use. Please note that the latest data is available at Phytozome.

Status

v.1.0. (June 1, 2007): The genome of Volvox carteri is estimated to be approximately 140 Mb and was sequenced to approximately 8X depth.

The current release contains a total of 15,544 predicted gene models produced at the JGI and is composed of a mixture of Volvox carteri f.nagariensis known genes mapped to the genomic sequence, gene models built by homology to known proteins from other model organisms and ab initio gene predictions as well as support from available Volvox carteri f.nagariensis EST and cDNA data.

Approximately 95% of Volvox carteri full-length cDNAs mapped to the v.1.0 assembly. Average gene length is 5.3 kb and average transcript length is 1.8 kb, with the average protein containing 558 amino acids. There are approximately 7.78 exons per gene averaging 236 bp each with intron spacing of 500 bp. Gene functions have been automatically assigned based on homology to known genes. Manual curation is underway.

Assembly

v.1.0 (March 2007): Approximately 1.9 Million shotgun reads were initially assembled using JAZZ. There are a total of 1,265 scaffolds, with a total length of 138 Mb composed of 11,403 contigs. Half of the assembly is contained in 33 scaffolds, all at least 1.49 Mb in length. The length-weighted mean contig size (L50) is 43 kb.

Collaborators

  • US Department of Energy Joint Genome Institute
  • David Kirk, Washington University, Department of Biology
  • Jim Umen,The Salk Institute, Plant Biology Laboratory
  • Ichiro Nishii, RIKEN, Nishii Initiative Research Unit
  • Patrick Ferris, The Salk Institute, Plant Biology Laboratory
  • Stephen Miller, Department of Biological Sciences, University of Maryland, Baltimore County
  • Kris Niyogi, Plant and Microbial Biology, UC Berkeley
  • Aurora Nedelcu, University of New Brunswick, Department of Biology
  • Armin Hallman, Universität Bielefeld, Abteilung für Zell-und Entwicklungsbiologie der Pflanzen

Links

Publications

Simon E. Prochnik, James Umen,Aurora M. Nedelcu,Armin Hallmann,Stephen M. Miller,Ichiro Nishii,Patrick Ferris,Alan Kuo,Therese Mitros,Lillian K. Fritz-Laylin,Uffe Hellsten,Jarrod Chapman,Oleg Simakov,Stefan A. Rensing,Astrid Terry,Jasmyn Pangilinan,Vladimir Kapitonov, Jerzy Jurka,Asaf Salamov,Harris Shapiro,Jeremy Schmutz,Jane Grimwood,Erika Lindquist,Susan Lucas,Igor V. Grigoriev,Rudiger Schmitt,David Kirk,Daniel S Rokhsar

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri Science Jul 9;329(5988):223-6.

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.