Status
The genome sequence of Rhizophagus irregularis B3 was not determined by the JGI.
The genome sequence was assembled with SPAdes (Nurk, Bankevich et al., 2013) and scaffolding was performed with SSPACE by Corradi Lab.
The genome was provided by INRA on January 20 2015. The annotation was done by Emmanuelle Morin of INRA using the JGI Annotation Pipeline.
This copy of the genome does not include the mitochondrial chromosome or genes.
Summary statistics for the Rhizophagus irregularis v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 124.89 |
| Sequencing read coverage depth | 0x |
| # of contigs | 16875 |
| # of scaffolds | 10461 |
| # of scaffolds >= 2Kbp | 5229 |
| Scaffold N50 | 732 |
| Scaffold L50 (Mbp) | 0.05 |
| # of gaps | 6414 |
| % of scaffold length in gaps | 4.2% |
| Three largest Scaffolds (Mbp) | 0.30, 0.26, 0.25 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | 454_ESTs | 365294 | 327322 | 89.6% |
| Ests | Sanger_ESTs | 40364 | 32582 | 80.7% |
| Other | 454_and_Sanger_EST_contigs | 25906 | 21947 | 84.7% |
| Other | CIFAR_B3_RNAseq_contigs | 22928 | 21888 | 95.5% |
| Other | Solexa_RNA_contigs | 26503 | 21679 | 81.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1392 | 1064 |
| transcript | 1044 | 785 |
| exon | 276 | 160 |
| intron | 127 | 81 |
| description: | ||
| protein length (aa) | 316 | 225 |
| exons per gene | 3.79 | 3 |
| # of gene models | 25164 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N
High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
New Phytol. 2018 Dec;220(4):1161-1171. doi: 10.1111/nph.14989
Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N
High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
New Phytol. 2018 Dec;220(4):1161-1171. doi: 10.1111/nph.14989
Funding
This project was not sequenced at the JGI.
