Supplemental Files for "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis"

Supplemental files for "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis". This data is linked to the bioRxiv pre-print doi: https://doi.org/10.1101/2022.10.19.511543, an updated version of which is in press at G3: Genes|Genomes|Genetics, and corresponds to the NCBI BioProject PRJNA885267 and NCBI BioSample SAMN31081226.

Nuclear genome assembly

Rhizophagus_irregularis_DAOM197198_assembly.fasta

Illumina and Illumina+Nanopore gene annotations

Rhizophagus_irregularis_DAOM197198_Illumina+ONT_curated.gff3

Rhizophagus_irregularis_DAOM197198_Illumina_curated.gff3

Illumina and Illumina+Nanopore functional gene annotations

Rhizophagus_irregularis_DAOM197198_annotations_Illumina+ONT.txt

Rhizophagus_irregularis_DAOM197198_annotations_Illumina.txt

Illumina and Illumina+Nanopore CDS sequences

Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina+ONT_curated.fa

Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina_curated.fa

Illumina and Illumina+Nanopore mRNA sequences

Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina+ONT_curated.fa

Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina_curated.fa

Illumina and Illumina+Nanopore protein sequences

Rhizophagus_irregularis_DAOM197198_proteins_Illumina+ONT_curated.fa

Rhizophagus_irregularis_DAOM197198_proteins_Illumina_curated.fa

GO terms for g:Profiler
Rhizophagus_irregularis_DAOM197198_Illumina+ONT_GOterms.gmt
*Or use token gp__xfGY_dQeI_yx4

Repetitive and transposable element library and annotation

Rhizophagus_irregularis_DAOM197198_curatedrepeatlibrary.fasta

Rhizophagus_irregularis_DAOM197198_repeatmasker.out

Rhizophagus_irregularis_DAOM197198_repeats.gff3

DNA methylome (sequenced from spores)

Rhizophagus_irregularis_DAOM197198_mCG_mods_frequency.tsv

Poly(A) signal and tail sequences

Rhizophagus_irregularis_DAOM197198_pasa_polyAsite_analysis.out

Rhizophagus_irregularis_DAOM197198_pasa_polyAsites.fasta

Small RNA annotation

Rhizophagus_irregularis_DAOM197198_sRNA.gff3

Rhizophagus_irregularis_DAOM197198_sRNA.tsv

Mitochondrial genome assembly and annotation

Rhizophagus_irregularis_DAOM197198_mtDNA.fasta

Rhizophagus_irregularis_DAOM197198_mtDNA.gff

R. irregularis phylostratigraphy

Rhizophagus_irregularis_DAOM197198_1432141_phyloranks.tsv

Rhizophagus_irregularis_DAOM197198_1432141_high-confidence_phyloranks.tsv

Mucoromycota fungi phylostratigraphy

Disdec1_101101_phyloranks.tsv

Geopyr1_50956_phyloranks.tsv

Gigmar1_4874_phyloranks.tsv

Morel2_1314771_phyloranks.tsv

Phybl2_4837_phyloranks.tsv

Radspe1_64574_phyloranks.tsv

Fatty acid synthase phylogeny

FAS_genes_muscle5_msa.fa (alignments)

FAS_genes.raxml.support (ML tree)