Status
The Rhizophagus irregularis A1 genome sequence and gene models have not been determined by the JGI, but were received from the laboratory of Nicolas Corradi at University of Ottawa on March 05, 2024. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 3408 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All of the original published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by the Corradi lab and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into MycoCosm. The JGI Annotation Pipeline was used to add functional annotation to the genes.
Genome Assembly | |
Genome Assembly size (Mbp) | 147.09 |
Sequencing read coverage depth | |
# of contigs | 250 |
# of scaffolds | 33 |
# of scaffolds >= 2Kbp | 33 |
Scaffold N50 | 14 |
Scaffold L50 (Mbp) | 4.76 |
# of gaps | 217 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 6.39, 6.20, 6.09 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1547 | 1254 |
transcript | 1220 | 963 |
exon | 286 | 155 |
intron | 102 | 80 |
description: | ||
protein length (aa) | 407 | 321 |
exons per gene | 4.26 | 3 |
# of gene models | 20492 |
Collaborators
Genome Reference(s)
Yildirir G, Sperschneider J, Malar C M, Chen ECH, Iwasaki W, Cornell C, Corradi N
Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
New Phytol. 2022 Feb;233(3):1097-1107. doi: 10.1111/nph.17842
Links
- JGI PhyloGroup Portals: Fungi Mucoromycota Glomeromycotina
- JGI EcoGroup Portals: Mycorrhizal Fungi Arbuscular Mycorrhizal Fungi