Status
[November 2018] The genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available on the Download page.
Summary statistics for the Tirmania nivea G3 v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 63.13 |
| Sequencing read coverage depth | 106.53x |
| # of contigs | 421 |
| # of scaffolds | 421 |
| # of scaffolds >= 2Kbp | 412 |
| Scaffold N50 | 32 |
| Scaffold L50 (Mbp) | 0.63 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.76, 1.55, 1.53 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 53996 | 47353 | 87.7% |
| Ests | est.fasta | 146880139 | 143812135 | 97.9% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1776 | 1506 |
| transcript | 1554 | 1291 |
| exon | 460 | 272 |
| intron | 95 | 65 |
| description: | ||
| protein length (aa) | 441 | 347 |
| exons per gene | 3.38 | 3 |
| # of gene models | 10591 |
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
Marqués-Gálvez JE, Miyauchi S, Paolocci F, Navarro-Ródenas A, Arenas F, Pérez-Gilabert M, Morin E, Auer L, Barry KW, Kuo A, Grigoriev IV, Martin FM, Kohler A, Morte A
Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle.
New Phytol. 2021 Mar;229(5):2917-2932. doi: 10.1111/nph.17044
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
Marqués-Gálvez JE, Miyauchi S, Paolocci F, Navarro-Ródenas A, Arenas F, Pérez-Gilabert M, Morin E, Auer L, Barry KW, Kuo A, Grigoriev IV, Martin FM, Kohler A, Morte A
Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle.
New Phytol. 2021 Mar;229(5):2917-2932. doi: 10.1111/nph.17044
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.
