Info • Pseudocercospora (Mycosphaerella) fijiensis v2.0

Status

v2.0 (May 2010)

The assembly release version 2.0 is an Arachne assembly that was improved based on markers of the genetic linkage map that were sequenced and aligned to the genome and is now in 56 main genome scaffolds. Roughly half of the genome is contained in 5 scaffolds all at least 5.9 MB in length.

v.1.0 (August 2007)

The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of ~7.11X. After trimming for vector and quality, 602,555 reads assembled into 395 main genome scaffolds totaling 73.4 MB. Roughly half of the genome is contained in 12 scaffolds all at least 1.99 MB in length.

Genome Assembly v1.0 v2.0
Scaffold count 382 56
All Contig count 5527 778
Scaffold sequence bases total 73.4 Mb 74.1 Mb
Scaffold sequence bases total 73.4 Mb 74.1 Mb
Scaffolded (Large) Contig sequence bases total 66.8 Mb 73.7 Mb
Estimated % sequence bases in gaps 8.9% 0.6%
Scaffold N50/L50 12/2.0 Mb 5/5.9 Mb
Contig N50/L50 446/39.4 Kb 99/210.7 Kb
Number of scaffolds > 50.0 Kb 78 28
% in scaffolds > 50.0 Kb 95.3% 99.8%
v2.0 (May 2010)

Annotation of the v2.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. The v1.0 gene catalog along with its manual curations was mapped to the v2.0 assembly and included in filtering. After filtering for EST support, completeness and homology support, a total of 13,903 genes were structurally and functionally annotated.

v1.0 (August 2007)

The v1.0 annotation was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness and homology support, a total of 10,316 genes were structurally and functionally annotated.

Nuclear Genome Annotation v1.0 v2.0
# gene models 10,316 13,107
Gene density 140.54 187.62
Avg.gene length 1629 nt 1833 nt
Avg. protein length 436 aa 427 aa
Avg. exon frequency 2.45 exons/gene 3.62 exons/gene
Avg. exon length 578 nt 395 nt
Avg. intron length 148 nt 154 nt
% complete gene models (with start and stop codons) 82% 88%
% genes with homology support 70% 74%
% genes with Pfam domains 48% 49%

Collaborators

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Arango Isaza RE, Diaz-Trujillo C, Dhillon B, Aerts A, Carlier J, Crane CF, V de Jong T, de Vries I, Dietrich R, Farmer AD, Fortes Fereira C, Garcia S, Guzman M, Hamelin RC, Lindquist EA, Mehrabi R, Quiros O, Schmutz J, Shapiro H, Reynolds E, Scalliet G, Souza M Jr, Stergiopoulos I, Van der Lee TA, De Wit PJ, Zapater MF, Zwiers LH, Grigoriev IV, Goodwin SB, Kema GH
Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control.
PLoS Genet. 2016 Aug;12(8):e1005876. doi: 10.1371/journal.pgen.1005876

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.