Status
Version2.0 (March 2009)
The assembly version 2.0 was built using Arachne assembler from WGS data and BAC-end sequences with ~9.7x coverage and the following assembly statistics.
Genomic assembly stats:
| Main genome scaffold total: | 115 |
| Main genome contig total: | 752 |
| Main genome scaffold sequence total: | 77.8 MB |
| Main genome contig sequence total: | 76.6 MB (-> 1.6% gaps) |
| Main genome scaffold N/L50: | 6/4.3 MB |
| Main genome contig N/L50: | 57/406.0 KB |
| % main genome in scaffolds > 50 KB: | 32 |
| % in scaffolds >50 KB: | 99.1% |
18576 gene models with annotations were mapped from v1.1 to current assembly. Finishing is in progress and the finished genome will be reannotated.
Version1.1 (August 2004)
The assembly version 1.1 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 9X. After trimming for vector and quality, over 1 Million reads assembled into 1810 scaffolds totaling over 86 Mbp. Roughly half of the genome is contained in 54 scaffolds all at least 463 Kb in length. The estimated genome size is 95 Mbp.
A total of 19,027 gene models was predicted in the assembly version 1.1 using the JGI automated annotation pipeline. Gene models and associated transcripts/proteins were predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. Conservation between the genomic sequences of P. sojae and P. ramorum provided additional support for the predicted gene models.
Collaborators
Brett Tyler, Ph.D., Virginia Bioinformatics Institute, Virginia Polytechnic and State University
