Spironucleus vortens
 


Status

~130Mbp ofS.vortens genome was sequenced, which corresponds to over 8X coverage for 15Mbp genome, which was initial genome size estimate. In addition, two EST libraries and 13 subclone fosmids were sequenced. The assembled genome reads form contigs on average ~2X. ~18% of the gene space is assembled based on analysis of aligned ESTs. Genome did not assemble possibly due to high polymorphism, much larger genome size, and/or unclonable regions of genome. A large portion of the genome consists of repetitive sequence. Currently no further sequencing is planned. In future, as technology advances and cheaper sequencing may help to improve the coverage of the S. vortens genome.

Assembly statistics:

  • Main genome total reads : 104,597
  • Main genome total number of scaffolds: 10,044
  • Main genome total length of scaffolds: 103.549582 Mb
  • Main genome N50 scaffold number: 678
  • Main genome N50 scaffold size: 37.044 Kb
  • Main genome total number of contigs: 20,839
  • Main genome total length of contigs: 33.497728 Mb
  • Main genome N50 contig number: 5,775
  • Main genome N50 contig size: 1.829 Kb
ESTs
    
 
LIBRARY: Stats            
Library Attempted Attempted Insertless Contam Passing Passing  
  ESTs Clones Clones(%) Clones(%) Clones(%) Diversity(%)  
CAPO 14592 7296 173( 2.4) 862( 11.8) 6148(84.3) 24.11  
CAPP 14592 7296 270( 3.7) 466( 6.4) 6500(89.1) 21.86  
All = (CAPO_CAPP) 29184 14592 443( 3.0) 1328( 9.1) 12648(86.7) 19.69  
Diversity"= Number clusters/Number passing clones
Clustering: Stats            
Library Number Number Number Clusters Clusters    
  Clusters Cons Singlet w/ one w/ > one Clusters Consensus
    Sequence Clusters Clone Clone 5'-3' 5'-3'
CAPO 1482 3094 98 851 533 613 473
CAPP 1421 1793 87 939 395 1212 1297
All = (CAPO_CAPP) 2491 4375 158 1572 742 1555 1582
 
 
 
 
     
Taxonomy    
Tax id:
   58336
Lineage:
   Eukaryota; Diplomonadida group; Diplomonadida; Hexamitidae; Hexamitinae; Spironucleus
     
Contacts    
JGI:
   Project Management Office
Collaborators:
   W. Zacheus Cande, University of California, Berkeley
     
     
Funding
  This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.