Info • Rhizophagus irregularis A5 v1.0

Status

The genome sequence of Rhizophagus irregularis A5 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) 131.46
Sequencing read coverage depth 0x
# of contigs 22262
# of scaffolds 14626
# of scaffolds >= 2Kbp 6599
Scaffold N50 920
Scaffold L50 (Mbp) 0.04
# of gaps 7636
% of scaffold length in gaps 4.9%
Three largest Scaffolds (Mbp) 0.35, 0.26, 0.22


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests 454_ESTs 365294 326809 89.5%
Ests Sanger_ESTs 40364 32602 80.8%
Other 454_and_Sanger_EST_contigs 25906 21815 84.2%
Other CIFAR_A5_RNAseq_contigs 17517 16765 95.7%
Other Solexa_RNA_contigs 26503 21530 81.2%


Gene Models FilteredModels1
length (bp) of: average median
gene 1343 1004
transcript 1012 743
exon 275 162
intron 125 81
description:
protein length (aa) 307 216
exons per gene 3.68 2
# of gene models 26585


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.