Info • Rhizophagus irregularis A4 v1.0

Status

The genome sequence of Rhizophagus irregularis A4 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) 138.30
Sequencing read coverage depth 0x
# of contigs 21308
# of scaffolds 11380
# of scaffolds >= 2Kbp 6440
Scaffold N50 909
Scaffold L50 (Mbp) 0.04
# of gaps 9928
% of scaffold length in gaps 4.2%
Three largest Scaffolds (Mbp) 0.32, 0.26, 0.25


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests 454_ESTs 365294 316253 86.6%
Ests Sanger_ESTs 40364 31482 78.0%
Other 454_and_Sanger_EST_contigs 25906 20665 79.8%
Other CIFAR_A4_RNAseq_contigs 23354 22012 94.3%
Other Solexa_RNA_contigs 26503 19959 75.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1398 1074
transcript 1038 771
exon 269 156
intron 128 81
description:
protein length (aa) 318 225
exons per gene 3.86 3
# of gene models 25760


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.