IGV Bundle for Rhizophagus irregularis DAOM-197198

Use these files to build your own genome browser for the "Rhiir3" Rhizophagus irregularis DAOM-197198 chromosome-scale genome assembly (PRJNA885267). Tracks available:

Gene annotation, based on Illumina and Nanopore RNA-Seq reads.
Gene models were curated by excluding genes with InterPro domains related to transposable elements.
File: Rhiir3_PRJNA885267_genes.gff3

Repeat annotation.
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.
File: Rhiir3_PRJNA885267_repeats.gff3

Highly methylated CG sites, called via direct Nanopore genomic DNA sequencing of R. irregularis spores. 
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).
File: Rhiir3_PRJNA885267_high_meth_CG.bed

Index for CG methylation sites.
File: Rhiir3_PRJNA885267_high_meth_CG.bed.idx

Nanopore RNA-Sequencing reads, poly(A)+ cDNA-PCR, from R. irregularis spores.
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).
File: Rhiir3_PRJNA885267_nano_cDNA.bam

Index for Nanopore RNA-Sequencing reads.
File: Rhiir3_PRJNA885267_nano_cDNA.bam.bai

Small RNA loci.
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).
File: Rhiir3_PRJNA885267_small_RNA_loci.gff3

Small RNA sequencing reads.
Shortstack small RNA-Seq alignments, with multi-mappers randomly distributed.
File: Rhiir3_PRJNA885267_small_RNA.bam

Index for small RNA sequencing reads.
File: Rhiir3_PRJNA885267_small_RNA.bam.bai