Status
Assembly v1 (March 2012) is a draft assembly of Solexa, 454, and Sanger gDNA reads. A total of 28371 scaffolds and 91.1 Mbp were assembled by INRA using CLC Genomic Workbench.
Summary statistics for the Rhizophagus irregulare v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 91.08 |
| Sequencing read coverage depth | 0x |
| # of contigs | 28405 |
| # of scaffolds | 28371 |
| # of scaffolds >= 2Kbp | 15535 |
| Scaffold N50 | 5997 |
| Scaffold L50 (kbp) | 4.19 |
| # of gaps | 38 |
| % of scaffold length in gaps | 0.3% |
| Three largest Scaffolds (Mbp) | 0.06, 0.06, 0.06 |
| RNAs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | 454_ESTs | 365294 | 291958 | 79.9% |
| Ests | Sanger_ESTs | 40364 | 29552 | 73.2% |
| RNA contigs | 454_and_Sanger_EST_contigs | 25906 | 18871 | 72.8% |
| RNA contigs | Combest_RNA_contigs | 121068 | 109128 | 90.1% |
| RNA contigs | Solexa_RNA_contigs | 26503 | 19252 | 72.6% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1188 | 933 |
| transcript | 890 | 667 |
| exon | 257 | 151 |
| intron | 123 | 81 |
| description: | ||
| protein length (aa) | 270 | 194 |
| exons per gene | 3.46 | 2 |
| # of gene models | 30282 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Bécard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22. doi: 10.1073/pnas.1313452110
Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Bécard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22. doi: 10.1073/pnas.1313452110
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.
