Info • Rhizophagus irregularis A1 v1.0
Please note that this organism is for archival use only. Please see the current Rhizophagus irregularis A1 v2.0 site for the latest data and information.

Status

The genome sequence of Rhizophagus irregularis A1 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) 125.87
Sequencing read coverage depth 0x
# of contigs 18943
# of scaffolds 11301
# of scaffolds >= 2Kbp 4959
Scaffold N50 682
Scaffold L50 (Mbp) 0.05
# of gaps 7642
% of scaffold length in gaps 4.7%
Three largest Scaffolds (Mbp) 0.29, 0.29, 0.26


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests 454_ESTs 365294 328353 89.9%
Ests Sanger_ESTs 40364 32662 80.9%
Other 454_and_Sanger_EST_contigs 25906 22090 85.3%
Other CIFAR_A1_RNAseq_contigs 23509 22463 95.6%
Other Solexa_RNA_contigs 26503 21882 82.6%


Gene Models FilteredModels1
length (bp) of: average median
gene 1350 1014
transcript 1017 748
exon 277 162
intron 127 81
description:
protein length (aa) 309 216
exons per gene 3.67 2
# of gene models 26659


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.