PchrysosporiumRP-78 – MATPredict report

Result

Mating type

undetermined: complete locus, high confidence, 13.5 kb on PchrRP-78_SC013. Gene order: beta_fg · HD1 · HD2 · MIP1.

Called loci 1

undetermined HD family · Basidiomycota

high confidence

Gene order on PchrRP-78_SC013. Scroll sideways to see the whole figure.

FungiDB release 71 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.

core MAT gene
conserved flank
search hit only

Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.

Location: PchrRP-78_SC013:1,063,437–1,076,948 · 13.5 kb
Own genes: PchrRP-78_SC013:1,063,437–1,076,948 · 13.5 kb
Locus: Complete locus: MAT gene(s) with their flanking genes.
Genes modelled: 4 of 4 gene hits
Nearest contig end: 158.7 kb
Region (samtools): PchrRP-78_SC013:1063437-1076948

Gene evidence

Gene	Role	Model	Identity %	E-value	Position (strand)	Exons	Reference record	FungiDB gene
beta_fg	conserved flank	hit onlyDIAMOND, proteome	56.7cov 76.4%	6.7e-49155 bits	1,063,437–1,064,779 +	–	192523_h97_HD_A1	AGR57_12112
HD1	core MAT	hit onlyDIAMOND, proteome	40.9cov 48.5%	7.1e-61206 bits	1,070,153–1,072,196 -	–	2822231_sb25_HD_A1	AGR57_12117
HD2	core MAT	hit onlyDIAMOND, proteome	37.4cov 66.4%	1.8e-62204 bits	1,072,398–1,074,098 +	–	2822231_sb25_HD_A1	AGR57_12118
MIP1	conserved flank	hit onlyDIAMOND, proteome	84.6cov 98.4%	< 1e-180989 bits	1,074,457–1,076,948 -	–	2822231_sb25_HD_A1	AGR57_12119

What was searched

Routing: By taxonomy. The genome's taxonomy falls inside a curated family's scope; only those families were searched.
Families searched: Basidiomycota:HD, Basidiomycota:PR
Genetic code: 1
Taxonomy: local NCBI taxonomy snapshot 2026-10-01

Families searched but not called

family	reason	best % of genes found	genes found
Basidiomycota:PR	best cluster carried 0 modelled gene(s), below the 2 required to report a locus; none of its genes could be modelled	50.0	pheromone_B44, fungal_mating_type_pheromone

Pheromone-receptor arrays

Receptor arrays occur for both mating and non-mating STE3-like receptors (the study found arrays holding paralogs beside the mating receptors in Coprinopsis cinerea and Schizophyllum commune), so array membership does not establish that a locus is a mating receptor. receptor_array_support is a flag on the evidence behind an array; it never changes a call, its confidence or its verification label. receptor_cassette_* fields describe pheromone-precursor cassette structure (2 or more strict-CAAX ORFs within 5 kb of a receptor locus; class C when that many of those ORFs also carry tblastn precursor homology). They are descriptive only: the CAAX scan is also what admits a PR call, so cassettes are circular as confirmation; own-species curated precursors are a self-hit for class C; tandem receptors may be merged into one locus. They never change a call, tier, label, confidence or count.

array	location	loci	calls	support	reasons
Basidiomycota:PR:PchrRP-78_SC005:948455-950020	PchrRP-78_SC005:948,455–950,020	1	0	unsupported	a single receptor locus; no pheromone-precursor homology hit; 0 strict-CAAX pheromone ORFs
Basidiomycota:PR:PchrRP-78_SC009:1117669-1128912	PchrRP-78_SC009:1,117,669–1,128,912	3	0	supported	array of 2 or more receptor loci

Withheld candidate loci 5

Places with some MAT-gene evidence that did not pass a quality gate. Most genomes have several. They are listed so a known locus can be checked against them, not because they are likely calls.

Reasons: too few of the family's genes found (3); fewer than 2 genes could be modelled (2).

Show the 5 withheld loci

Withheld loci (5)

family	location	idiomorph	genes	modelled	reason
PR	PchrRP-78_SC005:742,983–763,819	undetermined	pheromone_B44, fungal_mating_type_pheromone	0	fewer than 2 genes could be modelled
PR	PchrRP-78_SC018:282,227–314,583	undetermined	pheromone_B44, fungal_mating_type_pheromone	0	fewer than 2 genes could be modelled
PR	PchrRP-78_SC005:948,455–950,020	undetermined	pheromone_receptor	1	too few of the family's genes found
PR	PchrRP-78_SC009:314,863–315,431	undetermined	pheromone_receptor	1	too few of the family's genes found
PR	PchrRP-78_SC009:1,117,669–1,128,912	undetermined	pheromone_receptor	1	too few of the family's genes found

Provenance

Genome file: PchrysosporiumRP-78.genome.fasta
Assembly: 232 contigs · 35.1 Mb · N50 1.9 Mb
Genome SHA-256: ec093f93b4b69498c4b3860cf8fdc6a0a7e2c03f71e8175bc5a3b30a458cfe19
MATPredict: 0.8.1 (v0.8.1, 3a62e6302b)
Database: 86f18d232e4fe95d · 185 records
Taxonomy: local NCBI taxonomy snapshot 2026-10-01
Parameters: phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'genus', 'routing_taxid': 396331, 'routing_taxid_rank': 'family', 'flags': ['high_N'], 'gmg_version': 'gmg 0.3.2 (66055154a)', 'index': 'bfd-reps-2026.10.5-s20000.gmgi', 'index_sha256': '0f319567f1cab17643e1daf7ffdc0e3b312bd43913e351568108d67a4a19702c', 'index_spec': 'bfd-reps-2026.10.5-s20000.gmgi', 'note': 'GmG called phylum Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 396331', 'routed_by': 'family taxid 396331 (lineage)'}, genetic_code=1, min_hits=2, require_core_role=True, max_polished_clusters_per_family=6, polish_strong_identity=50.0, polish_core_pair=True, partial_core_policy=off, homothallic_policy=off, confidence_cap_policy=off, cross_family_policy=off, fallback_after_withheld_policy=off, strong_single_gene_policy=off, scoped_roster_policy=off, supported_min_bitscore=33.0
Run started: 2026-11-07T02:37:55Z
Run time: 80 s
Files: detection_report.yaml, detected_loci.gff3

Cite MATPredict as given in CITATION.cff at github.com/stajichlab/MATPredict. The reference records named in the gene tables are curated database entries; each record's metadata cites its source publication.

How to read this report

Idiomorph: The form of the mating-type locus a strain carries (for example MAT1-1 or MAT1-2, Plus or Minus). Basidiomycota HD and PR alleles are named after the reference they match.
High confidence: Every expected core MAT gene was found and modelled, with a conserved flanking gene where the family has one, on one contig.
Medium confidence: The core genes were found, but a gene could not be modelled, no conserved flank was found, or the locus is split (one step down).
Low confidence: A single isolated gene hit, or no core MAT gene.
Model status: Gene model: the reference protein was aligned to the genome to build the gene (exonerate, miniprot). Models differ: the two tools disagree on the structure; the alternate model is shown. Hit only: a search hit with no model, weaker evidence.
Identity: Percent amino-acid identity between the gene (or hit) and the closest reference protein.
Reference record: The curated database record whose protein matched best. Each record's metadata cites the publication or deposit it comes from.

Limits

MATPredict reads an assembly; it is not a mating assay. Two idiomorphs in one assembly can come from a homothallic species, a mixed culture or a merged diploid assembly.
Fragmented assemblies can split a locus or lose its flanking genes; an uncalled genome is weak evidence of absence.
Lineages with no curated record are searched with the whole phylum's references; family labels there are less reliable.