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

<p>Supplemental files for &quot;A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus&nbsp;Rhizophagus irregularis&quot;. This data is linked to the bioRxiv pre-print&nbsp;doi:&nbsp;https://doi.org/10.1101/2022.10.19.511543, an&nbsp;updated version of which is in press at&nbsp;G3: Genes|Genomes|Genetics, and corresponds to the&nbsp;NCBI BioProject&nbsp;PRJNA885267 and&nbsp;NCBI BioSample&nbsp;SAMN31081226.</p> <p>&nbsp;</p> <p><strong>Nuclear genome assembly</strong></p> <p>Rhizophagus_irregularis_DAOM197198_assembly.fasta</p> <p>&nbsp;</p> <p><strong>Illumina and Illumina+Nanopore gene&nbsp;annotations</strong></p> <p>Rhizophagus_irregularis_DAOM197198_Illumina+ONT_curated.gff3</p> <p>Rhizophagus_irregularis_DAOM197198_Illumina_curated.gff3</p> <p>&nbsp;</p> <p><strong>Illumina and Illumina+Nanopore functional gene annotations</strong></p> <p>Rhizophagus_irregularis_DAOM197198_annotations_Illumina+ONT.txt</p> <p>Rhizophagus_irregularis_DAOM197198_annotations_Illumina.txt</p> <p>&nbsp;</p> <p><strong>Illumina and Illumina+Nanopore CDS sequences</strong></p> <p><span>Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina+ONT_curated.fa</span></p> <p>Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina_curated.fa</p> <p>&nbsp;</p> <p><strong>Illumina and Illumina+Nanopore mRNA sequences</strong></p> <p>Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina+ONT_curated.fa</p> <p>Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina_curated.fa</p> <p>&nbsp;</p> <p><strong>Illumina and Illumina+Nanopore protein sequences</strong></p> <p><span>Rhizophagus_irregularis_DAOM197198_proteins_Illumina+ONT_curated.fa</span></p> <p>Rhizophagus_irregularis_DAOM197198_proteins_Illumina_curated.fa</p> <p>&nbsp;</p> <p><strong>GO terms for g:Profiler</strong><br> Rhizophagus_irregularis_DAOM197198_Illumina+ONT_GOterms.gmt<br> *Or use token&nbsp;gp__xfGY_dQeI_yx4</p> <p>&nbsp;</p> <p><strong>Repetitive and transposable element library and&nbsp;annotation</strong></p> <p>Rhizophagus_irregularis_DAOM197198_curatedrepeatlibrary.fasta</p> <p>Rhizophagus_irregularis_DAOM197198_repeatmasker.out</p> <p>Rhizophagus_irregularis_DAOM197198_repeats.gff3</p> <p>&nbsp;</p> <p><strong>DNA methylome (sequenced from spores)</strong></p> <p>Rhizophagus_irregularis_DAOM197198_mCG_mods_frequency.tsv</p> <p>&nbsp;</p> <p><strong>Poly(A) signal and tail sequences</strong></p> <p>Rhizophagus_irregularis_DAOM197198_pasa_polyAsite_analysis.out</p> <p>Rhizophagus_irregularis_DAOM197198_pasa_polyAsites.fasta</p> <p>&nbsp;</p> <p><strong>Small RNA annotation</strong></p> <p>Rhizophagus_irregularis_DAOM197198_sRNA.gff3</p> <p>Rhizophagus_irregularis_DAOM197198_sRNA.tsv</p> <p>&nbsp;</p> <p><strong>Mitochondrial genome assembly and annotation</strong></p> <p>Rhizophagus_irregularis_DAOM197198_mtDNA.fasta</p> <p>Rhizophagus_irregularis_DAOM197198_mtDNA.gff</p> <p>&nbsp;</p> <p><strong><em>R. irregularis</em>&nbsp;phylostratigraphy</strong></p> <p>Rhizophagus_irregularis_DAOM197198_1432141_phyloranks.tsv</p> <p>Rhizophagus_irregularis_DAOM197198_1432141_high-confidence_phyloranks.tsv</p> <p>&nbsp;</p> <p><strong>Mucoromycota fungi phylostratigraphy</strong></p> <p>Disdec1_101101_phyloranks.tsv</p> <p>Geopyr1_50956_phyloranks.tsv</p> <p>Gigmar1_4874_phyloranks.tsv</p> <p>Morel2_1314771_phyloranks.tsv</p> <p>Phybl2_4837_phyloranks.tsv</p> <p>Radspe1_64574_phyloranks.tsv</p> <p>&nbsp;</p> <p><strong>Fatty acid synthase phylogeny</strong></p> <p>FAS_genes_muscle5_msa.fa (alignments)</p> <p>FAS_genes.raxml.support (ML tree)</p>