Status
[December 2015] The Melampsora larici-populina v2.0 genome was assembled using ARACHNE. Misassemblies were identified using a map provided by Uffe Helsten which was based on 85 offspring, and has map position information at 29,168 unique positions in the genome. Scaffold breaks were identified using an abrupt change in the linkage group. A total of 62 breaks were made. Scaffolds were then oriented, ordered, and joined together using the map and assembled into 18 chromosomes. A total of 186 joins were made during this process.
Summary statistics for the Melampsora larici-populina v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 109.88 |
| Sequencing read coverage depth | 7.47x |
| # of contigs | 4520 |
| # of scaffolds | 511 |
| # of scaffolds >= 2Kbp | 486 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 5.82 |
| # of gaps | 4009 |
| % of scaffold length in gaps | 5.8% |
| Three largest Scaffolds (Mbp) | 8.57, 8.00, 7.40 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | SangerESTclusters | 11535 | 8470 | 73.4% |
| Ests | est.fasta | 522244426 | 491776833 | 94.2% |
| Other | Trinity_assembled_transcripts | 57498 | 33208 | 57.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1468 | 1156 |
| transcript | 1110 | 846 |
| exon | 254 | 153 |
| intron | 108 | 81 |
| description: | ||
| protein length (aa) | 339 | 255 |
| exons per gene | 4.37 | 3 |
| # of gene models | 19550 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Persoons A, Maupetit A, Louet C, Andrieux A, Lipzen A, Barry KW, Na H, Adam C, Grigoriev IV, Segura V, Duplessis S, Frey P, Halkett F, De Mita S
Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.
Genome Biol Evol. 2022 Jan 4;14(1):. doi: 10.1093/gbe/evab279
Persoons A, Maupetit A, Louet C, Andrieux A, Lipzen A, Barry KW, Na H, Adam C, Grigoriev IV, Segura V, Duplessis S, Frey P, Halkett F, De Mita S
Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.
Genome Biol Evol. 2022 Jan 4;14(1):. doi: 10.1093/gbe/evab279
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.
