Status
The genome sequence of Rhizophagus diaphanum was not determined by the JGI. The genome was provided by INRA, assembled with AllpathLG, and annotated by Emmanuelle Morin (INRA) using the JGI Annotation Pipeline. This copy of the genome does not include the mitochondrial chromosome or genes.
Summary statistics for the Rhizophagus diaphanum v1.0 release are below.| Genome Assembly | |
| Genome Assembly size (Mbp) | 125.88 |
| Sequencing read coverage depth | 50x |
| # of contigs | 11501 |
| # of scaffolds | 2764 |
| # of scaffolds >= 2Kbp | 2027 |
| Scaffold N50 | 269 |
| Scaffold L50 (Mbp) | 0.14 |
| # of gaps | 8737 |
| % of scaffold length in gaps | 12.5% |
| Three largest Scaffolds (Mbp) | 0.69, 0.59, 0.54 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 200870252 | 193099662 | 96.1% |
| Other | Rhidi1_RNA_contigs | 74778 | 68851 | 92.1% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1487 | 1227 |
| transcript | 1096 | 877 |
| exon | 272 | 159 |
| intron | 131 | 82 |
| description: | ||
| protein length (aa) | 330 | 250 |
| exons per gene | 4.04 | 3 |
| # of gene models | 23252 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, de la Providencia I, Ndikumana S, Beaudet D, Hainaut M, Drula E, Kuo A, Tang N, Roy S, Viala J, Henrissat B, Grigoriev IV, Corradi N, Roux C, Martin FM
Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.
New Phytol. 2019 May;222(3):1584-1598. doi: 10.1111/nph.15687
Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, de la Providencia I, Ndikumana S, Beaudet D, Hainaut M, Drula E, Kuo A, Tang N, Roy S, Viala J, Henrissat B, Grigoriev IV, Corradi N, Roux C, Martin FM
Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.
New Phytol. 2019 May;222(3):1584-1598. doi: 10.1111/nph.15687
Funding
This project was not sequenced at the JGI.
