Status
[March 2016] The Melampsora allii-populina 12AY07 genome was sequenced using the PacBio platform and assembled together with Falcon version 20150310 (https://github.com/PacificBiosciences/FALCON), improved with finisherSC (Lam et al., 2014), then polished with Quiver version smrtanalysis_2.3.0 (Chin et al., 2013).
Summary statistics for the Melampsora allii-populina
12AY07 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 335.73 |
| Sequencing read coverage depth | 104.0x |
| # of contigs | 3637 |
| # of scaffolds | 3637 |
| # of scaffolds >= 2Kbp | 3633 |
| Scaffold N50 | 440 |
| Scaffold L50 (Mbp) | 0.19 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.29, 1.28, 1.25 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 174869929 | 146919428 | 84.0% |
| Ests | RNNotator_assembled_Illumina_ESTs | 32512 | 29705 | 91.4% |
| Gene Models | FilteredModels3 | |
| length (bp) of: | average | median |
| gene | 1495 | 1190 |
| transcript | 1118 | 851 |
| exon | 248 | 156 |
| intron | 109 | 80 |
| description: | ||
| protein length (aa) | 337 | 250 |
| exons per gene | 4.51 | 4 |
| # of gene models | 23089 |
Collaborators
Sebastien Duplessis, INRA, FR
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.
