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14 results for “Rhizophagus irregularis”
IGV Bundle for Rhizophagus irregularis DAOM-197198
<p>Use these files to build your own genome browser for the "Rhiir3" <em>Rhizophagus irregularis</em> DAOM-197198 chromosome-scale genome assembly (PRJNA885267). Tracks available:</p> <p><strong>Gene annotation, based on Illumina and Nanopore RNA-Seq reads. </strong><br> Gene models were curated by excluding genes with InterPro domains related to transposable elements.<br> File: Rhiir3_PRJNA885267_genes.gff3</p> <p><strong>Repeat annotation. </strong><br> The repeat library was made using EDTA (Ou et al., 2019), and curated by excluding consensus sequences with InterPro domains of known cellular genes. Repeats were then masked using RepeatMasker (parameters -s -no_is -norna -nolow -div 40) (Smit et al., 2015). Unclassified repeats are grey-coloured and repeats classified into transposable elements categories are colour-coded: LINEs are blue, DNA transposons are pink and LTRs are green.<br> File: Rhiir3_PRJNA885267_repeats.gff3</p> <p><strong>Highly methylated CG sites, called via direct Nanopore genomic DNA sequencing of <em>R. irregularis </em>spores.<em> </em></strong><br> 161Gb of raw FAST5 files obtained from three R9.4.1 Nanopore flow cells were basecalled with Guppy5, producing 985,449 reads which were successfully processed by tombo (Stoiber et al., 2017) and used by DeepSignal2 (Ni et al., 2019) to extract CG motifs and to call 5mC modifications using a human model (model.dp2.CG.R9.4_1D.human_hx1.bn17_sn16.both_bilstm.b17_s16_epoch4.ckpt. Only CG sites with >80% 5mC are shown, and the track indicates methylation ratios measured as a fraction of 1 (0.80 to 1.00).<br> File: Rhiir3_PRJNA885267_high_meth_CG.bed</p> <p><strong>Index for CG methylation sites.</strong><br> File: Rhiir3_PRJNA885267_high_meth_CG.bed.idx</p> <p><strong>Nanopore RNA-Sequencing reads, poly(A)+ cDNA-PCR, from <em>R. irregularis</em> spores. </strong><br> Reads were trimmed of adapters and cleaned with seqclean to remove a percentage of undetermined bases, polyA tails, overall low complexity sequences and short terminal matches. Cleaned sequences were then mapped using minimap2 (options: -G max intron length=3000, -ax, map-ont).<br> File: Rhiir3_PRJNA885267_nano_cDNA.bam</p> <p><strong>Index for Nanopore RNA-Sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_nano_cDNA.bam.bai</p> <p><strong>Small RNA loci.</strong><br> 70,956,710 small RNA-Seq reads from two replicates of oxidised and two replicates of column-purified spore RNA (Dallaire et al., 2021) were used to run ShortStack (Axtell, 2013) (parameters --dicermin 20 --dicermax 27 --foldsize 300 --pad 200 --mincov 10.0rpm --strand_cutoff 0.8 --mmap r).<br> File: Rhiir3_PRJNA885267_small_RNA_loci.gff3</p> <p><strong>Small RNA sequencing reads.</strong><br> Shortstack small RNA-Seq alignments, with multi-mappers randomly distributed.<br> File: Rhiir3_PRJNA885267_small_RNA.bam<br> <br> <strong>Index for small RNA sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_small_RNA.bam.bai</p>
Data described in the article "Unraveling the diversity of hyphal explorative traits among Rhizophagus irregularis genotypes"
<p>The dataset includes supplementary Figures, tables and the results of two experiments published in the study titled "Unraveling the diversity of hyphal explorative traits among Rhizophagus irregularis genotypes", available here: https://doi.org/10.1007/s00572-024-01154-8</p> <p>The study compares seven homokaryotic isolates (genotypes) of Rhizophagus irregularis, aiming to characterize the range of intraspecific variability with respect to hyphal exploration of organic nitrogen (N) resources, and N supply to plants. Two experiments (one in vitro and one in open pots) were conducted, and 15N-chitin as the isotopically labeled organic N source was used.</p> <p>Experiment 1 (in vitro), mycelium of all arbuscular mycorrhizal (AM) fungal genotypes transferred a higher amount of 15N to the plants than the passive transfer of 15N measured in the non-mycorrhizal (NM) controls. Noticeably, certain genotypes (e.g., LPA9) showed higher extraradical mycelium biomass production but not necessarily greater 15N acquisition than the others. </p> <p>Experiment 2 (in pots) highlighted that some of the AM fungal genotypes (e.g., MA2, STSI) exhibited higher rates of targeted hyphal exploration of chitin-enriched zones, indicative of distinct N exploration patterns from the other genotypes. Dataset contain photos and other recorded parameters during the experiment 1 and experiment 2.</p>
Supplemental Files for "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis"
<p>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.</p> <p> </p> <p><strong>Nuclear genome assembly</strong></p> <p>Rhizophagus_irregularis_DAOM197198_assembly.fasta</p> <p> </p> <p><strong>Illumina and Illumina+Nanopore gene annotations</strong></p> <p>Rhizophagus_irregularis_DAOM197198_Illumina+ONT_curated.gff3</p> <p>Rhizophagus_irregularis_DAOM197198_Illumina_curated.gff3</p> <p> </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> </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> </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> </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> </p> <p><strong>GO terms for g:Profiler</strong><br> Rhizophagus_irregularis_DAOM197198_Illumina+ONT_GOterms.gmt<br> *Or use token gp__xfGY_dQeI_yx4</p> <p> </p> <p><strong>Repetitive and transposable element library and 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> </p> <p><strong>DNA methylome (sequenced from spores)</strong></p> <p>Rhizophagus_irregularis_DAOM197198_mCG_mods_frequency.tsv</p> <p> </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> </p> <p><strong>Small RNA annotation</strong></p> <p>Rhizophagus_irregularis_DAOM197198_sRNA.gff3</p> <p>Rhizophagus_irregularis_DAOM197198_sRNA.tsv</p> <p> </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> </p> <p><strong><em>R. irregularis</em> phylostratigraphy</strong></p> <p>Rhizophagus_irregularis_DAOM197198_1432141_phyloranks.tsv</p> <p>Rhizophagus_irregularis_DAOM197198_1432141_high-confidence_phyloranks.tsv</p> <p> </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> </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>
RirC3: Rhizophagus irregularis reference genome and annotation
<p>Reference genome assembly of <em>Rhizophagus irregularis</em> isolate C3, made with PacBio Sequel II SMRT sequencing, and polished with Illumina reads. Annotation was produced with FunAnnotate.</p>
Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
<p>This repository contains annotations for the strains of <em>R. irregularis</em> chromosome assemblies.</p>
Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis
GEO Series GSE117158. Populus trichocarpa; Populus deltoides. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-Physiological and molecular responses of maize to the arbuscular mycorrhizla fungus 5AMF) Rhizophagus i
GEO Series GSE235654. Zea mays. 48 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
GEO Series GSE172187. Rhizophagus irregularis. 35 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis
GEO Series GSE129059. Triticum aestivum. 6 samples. Type: Expression profiling by high throughput sequencing.
Incidence of phosphate variations on nutrient transports in a symbiocosm formed by poplar, sorghum and Rhizophagus irregularis.
GEO Series GSE138316. Populus trichocarpa; Rhizophagus irregularis; Sorghum bicolor. 27 samples. Type: Expression profiling by high throughput sequencing.
Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis
GEO Series GSE99655. Rhizophagus irregularis. 18 samples. Type: Expression profiling by high throughput sequencing.
Rhizophagus irregularis gene regulation in response to rice root exudates
GEO Series GSE65595. Rhizophagus irregularis. 21 samples. Type: Expression profiling by high throughput sequencing.
Small RNA sequencing in tomato roots with and without Rhizophagus irregularis
GEO Series GSE76204. Solanum lycopersicum. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Rhizophagus irregularis gene regulation in early steps of AMF-plant symbiosis
GEO Series GSE67913. Rhizophagus irregularis DAOM 181602=DAOM 197198. 30 samples. Type: Expression profiling by high throughput sequencing.
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