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MAT discovery: Taphrinomycotina, Allomyces and unsearched-lineage probes - #353

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taphrino-probe

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MAT discovery: Taphrinomycotina, Allomyces and unsearched-lineage probes#353
hyphaltip wants to merge 22 commits into
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taphrino-probe

Commits on Nov 14, 2026
- Note: MAT discovery strategy and Taphrinomycotina detector probe
  
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  774157e
- Note: correct genome counts in the Taphrinomycotina table
  
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  a45bbc1
- Allomyces flank-first idiomorph probe, unsearched-lineage survey and gap-lineage scan
  
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  0382117
- Note: fix escaped backticks
  
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  5f6502c
- Taphrinomycotina PM leads: Pfam and gene-order follow-up, rescan of 10 empty genomes, correct genome count
  
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  4edf4a0
- Note: retract PM leads statement where it was made
  
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  3e6279f
- Taphrinomycotina matPi search with positive control, lead follow-up in other lineages, strategy status
  
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  f1bf9da
- Scan genomes outside the first surveys: 3 annotated, 4 with Augustus gene models; status of the rest
  
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  f486399
- Note: correct genome counts of the unscanned set and the candidate-count comparison
  
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  aeda7f2
- Note: correct Synchytrium and Globomyces assembly details
  
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  c13e9f9
- Coverage recount by locus tag, Augustus scans of 7 more assemblies, Globomyces conservation test
  
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  655d980
- Note: correct the Microsporidia count in the unscanned set
  
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  0b18f25
- Note: why the last 50 genomes cannot be scanned
  
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  8085d32
- Taphrinomycotina: genome-level matPi search finds an HMG + homeodomain pair in 6 of 17 genomes; retract earlier statements
  
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  dc70112
- Note: correct genome counts and the T. communis region check in the matPi section
  
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  c84ea42
- Taphrinomycotina: gene models and cross-genome orthology of the HMG + homeodomain pair; fix ORF end coordinate
  
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  162ded2
- Note: correct comparison counts in the orthology section
  
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  f114bb7
- Taphrinomycotina: RNA-seq shows the HMG and homeodomain genes of the PM-like locus are transcribed in T. deformans A2 and P. lactucae-debilis 12-1054
  
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  6e13b7e
- Taphrinomycotina: StringTie transcript assembly at the HMG + homeodomain locus
  
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  48b30cf
- Note: trace the curated T. deformans matPi to a translated tblastn region
  
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  981414e
- Taphrinomycotina: infer library strandedness; the homeodomain gene of the P. lactucae-debilis locus is on the minus strand like the HMG gene
  
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  63e0d53
Commits on Nov 15, 2026
- Annotation-free tblastn search of 48 fragmentary assemblies: no HMG + homeodomain pair on one contig
  
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  6f84fbc

Commits

Commits on Nov 14, 2026

Commits on Nov 15, 2026