Status
Assembly v2 (January 2015) is an improved draft assembly, drafted from Illumina gDNAs using AllPathsLG and then improved with PacBio gDNAs using PBJelly.
Summary statistics for the Hydnum rufescens UP504 v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 67.14 |
| Sequencing read coverage depth | 102x |
| # of contigs | 2013 |
| # of scaffolds | 1072 |
| # of scaffolds >= 2Kbp | 817 |
| Scaffold N50 | 99 |
| Scaffold L50 (Mbp) | 0.22 |
| # of gaps | 941 |
| % of scaffold length in gaps | 3.6% |
| Three largest Scaffolds (Mbp) | 0.92, 0.76, 0.67 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 57141 | 54427 | 95.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1475 | 1167 |
| transcript | 1131 | 881 |
| exon | 213 | 140 |
| intron | 82 | 63 |
| description: | ||
| protein length (aa) | 327 | 238 |
| exons per gene | 5.32 | 4 |
| # of gene models | 18665 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sánchez-GarcÃa M, Morin E, Andreopoulos B, Barry KW, Bonito G, Buée M, Carver A, Chen C, Cichocki N, Clum A, Culley D, Crous PW, Fauchery L, Girlanda M, Hayes RD, Kéri Z, LaButti K, Lipzen A, Lombard V, Magnuson J, Maillard F, Murat C, Nolan M, Ohm RA, Pangilinan J, Pereira MF, Perotto S, Peter M, Pfister S, Riley R, Sitrit Y, Stielow JB, SzöllÅ‘si G, ŽifÄáková L, Å tursová M, Spatafora JW, Tedersoo L, Vaario LM, Yamada A, Yan M, Wang P, Xu J, Bruns T, Baldrian P, Vilgalys R, Dunand C, Henrissat B, Grigoriev IV, Hibbett D, Nagy LG, Martin FM
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Nat Commun. 2020 Oct 12;11(1):5125. doi: 10.1038/s41467-020-18795-w
Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sánchez-GarcÃa M, Morin E, Andreopoulos B, Barry KW, Bonito G, Buée M, Carver A, Chen C, Cichocki N, Clum A, Culley D, Crous PW, Fauchery L, Girlanda M, Hayes RD, Kéri Z, LaButti K, Lipzen A, Lombard V, Magnuson J, Maillard F, Murat C, Nolan M, Ohm RA, Pangilinan J, Pereira MF, Perotto S, Peter M, Pfister S, Riley R, Sitrit Y, Stielow JB, SzöllÅ‘si G, ŽifÄáková L, Å tursová M, Spatafora JW, Tedersoo L, Vaario LM, Yamada A, Yan M, Wang P, Xu J, Bruns T, Baldrian P, Vilgalys R, Dunand C, Henrissat B, Grigoriev IV, Hibbett D, Nagy LG, Martin FM
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Nat Commun. 2020 Oct 12;11(1):5125. doi: 10.1038/s41467-020-18795-w
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.
