Status
(Mar 2016) The Hymenopellis radicata IJFM A160 genome was sequenced using PacBio, assembled with Falcon, improved with finisherSC, polished with Quiver, and annotated with the JGI annotation pipeline.
The JGI annotation pipeline identified 6,316 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 Hymenopellis radicata v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 78.59 |
| Sequencing read coverage depth | |
| # of contigs | 1968 |
| # of scaffolds | 1968 |
| # of scaffolds >= 2Kbp | 1877 |
| Scaffold N50 | 195 |
| Scaffold L50 (Mbp) | 0.10 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.28, 0.93, 0.74 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 55564 | 48816 | 87.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1454 | 1212 |
| transcript | 1179 | 982 |
| exon | 223 | 142 |
| intron | 66 | 53 |
| description: | ||
| protein length (aa) | 345 | 277 |
| exons per gene | 5.29 | 4 |
| # of gene models | 27481 |
Collaborators
José María Barrasa, Universidad de Alcalá, Spain
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ruiz-Dueñas FJ, Barrasa JM, Sánchez-GarcÃa M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, RamÃrez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, MartÃnez AT
Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.
Mol Biol Evol. 2021 Apr 13;38(4):1428-1446. doi: 10.1093/molbev/msaa301
Ruiz-Dueñas FJ, Barrasa JM, Sánchez-GarcÃa M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, RamÃrez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, MartÃnez AT
Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.
Mol Biol Evol. 2021 Apr 13;38(4):1428-1446. doi: 10.1093/molbev/msaa301
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.
