Info • Rhizophagus irregularis C2 v1.0
Please note that this organism is for archival use only. Please see the current Rhizophagus irregularis C2 site for the latest data and information.

Status

The genome sequence of Rhizophagus irregularis C2 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) 122.97
Sequencing read coverage depth 0x
# of contigs 16871
# of scaffolds 10857
# of scaffolds >= 2Kbp 5759
Scaffold N50 866
Scaffold L50 (Mbp) 0.04
# of gaps 6014
% of scaffold length in gaps 4.2%
Three largest Scaffolds (Mbp) 0.27, 0.23, 0.20


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests 454_ESTs 365294 323084 88.4%
Ests Sanger_ESTs 40364 32138 79.6%
Other 454_and_Sanger_EST_contigs 25906 21364 82.5%
Other CIFAR_C2_RNAseq_contigs 121802 72295 59.4%
Other Solexa_RNA_contigs 26503 20919 78.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1340 1031
transcript 1012 760
exon 274 163
intron 124 81
description:
protein length (aa) 299 210
exons per gene 3.69 3
# of gene models 26756


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

Funding

This project was not sequenced at the JGI.