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Info • Fragilariopsis cylindrus CCMP 1102

Status

v1.0 (November 2008): This Fragilariopsis cylindrus CCMP 1102 genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. Nuclear genome sequence annotation from this draft assembly is from the JGI Genome Annotation Pipeline and custom analyses.

Summary statistics for the Fragilariopsis_cylindrus CCMP 1102 v1.0 release:

Nuclear Genome Assembly v1.0
Nuclear genome size(Mbp) 80,5
Sequencing read coverage depth 7.25x
# of contigs 4602
# of scaffolds 271
# of nuclear scaffolds >50 Kbp 118
Nuclear scaffold N/L50 16/1.3 MB
Configs N/L50 164/78.2 KB
% genome in scaffolds >50 Kbp 98.4 %
% genome in gaps 5.4 %
% genome in repeats 4.3 %


ESTs Data set # sequences # mapped to genome % mapped to genome Notes
EST clusters Fracy1_EstClusters.fasta 9,122 7,955 87% Consensus sequences, one per cluster, for Fracy1_Ests
ESTs Fracy1_Ests.fasta 21,526 19,924 93% Pooled ESTs for T. terrestris, sequenced at JGI plus ~3,000 ESTs downloaded from GenBank
Gene Models v1.01
length (bp) of: average
gene 1572.35
transcript 1292.94
exon 615.29
intron 255.7
description:
protein length(aa) 408.64
exons per gene 2.1
# of gene models 27137
% gene models with :
nr homology support
EST support
PFAM domains
67%
30%
42%

Collaborators

  • Thomas Mock, Univ. of Washington
  • Micaela Parker, Univ. of Washington
  • E. Virginia Armbrust, Univ. of Washington
  • Klaus Valentin, Alfred-Wegener Inst. for Polar and Marine Research
  • Chris Bowler, Ecole Normale Superieure

Genome Reference(s)

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.