Genome Browser (instructions)

Genome Annotation (High-Quality genes)

Genome Overview (Genes vs. TEs - idiogram map)

Annotation Features and Functional Results

BLAST

BLAST genome, proteins, CDS, and gene models.

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OrthoVenn3

Pre-Computed OrthoVenn3 analyses across close-related species.

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Functional Annotation

Functional Annotation Plots: EC numbers, GOs, Transposable elements and others

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PASA

Program to Assemble Spliced Alignments Web Portal.  Summary report of the annotation (EVidence Modeler).

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FungiSMASH

Pre-computed fungiSMASH providing the annotation and analysis of secondary metabolite biosynthesis gene clusters.

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Dowload genomic and annotation data

Genome Sequence (fasta) | mtDNA ( fasta)
Annotation (gene models and functional annotation) (gff3 file)
Genes (fasta) | Proteins (fasta) | CDS (fasta)
Transposable Elements Annotation (gff3 file) | (FASTA)
PASA Assemblies (gff3) | (fasta)
RNAseq aligned data: fruiting body (bam)
RNAseq aligned data: mycelium (bam)
RNAseq aligned data: primordium (bam)

The data is also avaliable at GenBank and Zenodo

PRJ926637

Genome Browser Content and Instructions

jBrowser2 is a platform for visualizing genomic data. The  A. subrufescens genome browser contains the following tracks:  a) the gene models accompanied by annotation integrated in InterProScan visualization of each coding region; b) Transposable Elements and Repeats Annotation; c) PASA assemblies; d) tRNA and rRNA annotation ; and e) Aligned public available RNAseq data from different tissues (PRJNA305463 ): fruiting-body, mycelium, and primordium.
Use the "open track selector" to navigate into the different and avaliable tracks.

About

Agaricus subrufescens is a species of mushroom, commonly known as almond mushroom, mushroom of the sun, God's mushroom, mushroom of life, royal sun agaricus, jisongrong, or himematsutake and by a number of other names. Agaricus subrufescens is edible, with a somewhat sweet taste and a fragrance of almonds (see more on wikipedia ).

Genome Facts

- Genome Size: 44,531,294 bp;
- Number of chromosomes: 13 (31 unplaced sequences) and 131,367bp mitogenome;
- Number of genes: 14,332 (18,250 CDS);
- Gene vs. TEs content:  64.6% of genome is covered by genes and 23.41% is covered by TEs.
- BUSCO score genome: C:96.5%[S:92.2%,D:4.3%],F:0.4%,M:3.1%,n:3870 (agaricales_odb10).
- BUSCO score annotation: C:97.5%[S:80.2%,D:17.3%],F:0.6%,M:1.9%,n:3870 (agaricales_odb10)

Reference: Carlos Godinho de Abreu, Luiz Fernando Wurdig Roesch, Fernando Dini Andreote, Saura Rodrigues Silva, Tatiana Silveira Junqueira de Moraes, Diego Cunha Zied, Félix Gonçalves de Siqueira, Eustáquio Souza Dias, Alessandro M. Varani, Victor Satler Pylro. Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: A Resource for fungal biology and biotechnology. Research in Microbiology, 2023 -  https://doi.org/10.1016/j.resmic.2023.104116.

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