Status
(Apr 2016) The Rickenella fibula IJFM A160 v1.0 genome was sequenced using PacBio, assembled together with Falcon, improved with finisherSC, polished with Quiver, and annotated using the JGI annotation pipeline.
The annotation pipeline identified 3,898 gene models as possible diploid alleles, and excluded them from the filtered model/gene catalog set. These models are shown in the track "secondary_alleles", and are available from the download page.
Summary statistics for the Rickenella fibula v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 59.35 |
| Sequencing read coverage depth | 91.45X |
| # of contigs | 529 |
| # of scaffolds | 529 |
| # of scaffolds >= 2Kbp | 527 |
| Scaffold N50 | 35 |
| Scaffold L50 (Mbp) | 0.40 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.31, 1.77, 1.76 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 86187 | 77953 | 90.4% |
| Ests | est.fasta | 151463576 | 144660220 | 95.5% |
| Gene Models | FilteredModels5 | |
| length (bp) of: | average | median |
| gene | 1665 | 1412 |
| transcript | 1336 | 1119 |
| exon | 231 | 140 |
| intron | 71 | 58 |
| description: | ||
| protein length (aa) | 391 | 314 |
| exons per gene | 5.77 | 4 |
| # of gene models | 18897 |
Collaborators
Hailee Korotkin, University of Tennessee
Joseph W. Spatafora, Oregon State University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Korotkin HB, Swenie RA, Miettinen O, Budke JM, Chen KH, Lutzoni F, Smith ME, Matheny PB
Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.
Am J Bot. 2018 Nov;105(11):1869-1887. doi: 10.1002/ajb2.1183
Korotkin HB, Swenie RA, Miettinen O, Budke JM, Chen KH, Lutzoni F, Smith ME, Matheny PB
Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.
Am J Bot. 2018 Nov;105(11):1869-1887. doi: 10.1002/ajb2.1183
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.
