serinales_vs_pichiales_v2 — NovInvenio reports

Lineage-specific gene analysis · one folder, three interactive reports

Notes

Revision of serinales_vs_pichiales. Babjeviella inositovora is an outgroup here (it carries only 23.3% of the original 2,995 IN candidates, so it sits outside the rest of Serinales). Dropped for low added information: Candida dubliniensis, C. tropicalis, Suhomyces tanzawaensis, Hyphopichia burtonii (IN); Eremothecium gossypii, Ogataea parapolymorpha, Eeniella nana (OUT). 13 IN and 13 OUT species.

Reports

Each page is self-contained — open it directly, no network needed.

Novelty candidatesLineage-specific genes: present across the ingroup, absent from every outgroup proteome. Core genesNear-universally conserved genes shared by essentially every proteome, ingroup and outgroup. Candidate gene lossesGene families conserved across the outgroups but (nearly) absent from the ingroup. Functional enrichment (novelty)Pfam, InterPro and GO term enrichment of the novelty candidates against the proteome background. Functional enrichment (loss)Pfam, InterPro and GO term enrichment of the loss candidates against the proteome background.

Species tree

Species tree

phyling (FastTree, consensus of 10 single-marker trees; top 10 markers by treeness/RCV), fungi_odb12. Rooted on the OUT group (monophyletic).

Run summary

Parameters and proteomes from config.csv.

Ingroup proteomes
13
Outgroup proteomes
13
Search tool
diamond
Ingroup min fraction
0.75
Outgroup min fraction
0.75
Loss ingroup max fraction
0
Core min fraction
0.95
Pipeline version
v0.7.0+gd03f5a2 (dev)

Ingroup (13)

Genes are called lineage-specific relative to this clade.

ShortSpeciesTaxon group
CandalbiCandida albicans ATCC MYA-2876Serinales_Debaryomycetaceae
LoddelonLodderomyces elongisporus NRRL YB-4239Serinales_Debaryomycetaceae
MeyeguilMeyerozyma guilliermondii NRRL Y-324Serinales_Debaryomycetaceae
DebahansDebaryomyces hansenii IGC 2968Serinales_Debaryomycetaceae
SchestipScheffersomyces stipitis NRRL Y-11545Serinales_Debaryomycetaceae
SpatpassSpathaspora passalidarum 11-Y1Serinales_Debaryomycetaceae
CandtenuCandida tenuis VKM Y-70Serinales_Debaryomycetaceae
DiutrugoDiutina rugosaSerinales_other
YamajaroYamadazyma jarooniiSerinales_other
CandauriCandidozyma aurisSerinales_other
ClavlusiClavispora lusitaniae ATCC 42720Serinales_other
MetsbicuMetschnikowia bicuspidataSerinales_other
LizasparLizanozyma spartinaeSerinales_other

Outgroup (13)

Background proteomes used to exclude broadly conserved genes.

ShortSpeciesTaxon group
BabjinosBabjeviella inositovoraSerinales_Babjeviella_outgroup
KomaphafKomagataella phaffii ATCC 20864Pichiales
KuracapsKuraishia capsulataPichiales
PichmembPichia membranifaciensPichiales
PichkudrPichia kudriavzeviiPichiales
BretnaarBrettanomyces naardenensisPichiales
OgatpolyOgataea polymorphaPichiales
PachtannPachysolen tannophilusAlaninales
SacccereSaccharomyces cerevisiae S288cSaccharomycetaceae
KluylactKluyveromyces lactis WM37Saccharomycetaceae
LachtherLachancea thermotolerans NRRL Y-8284Saccharomycetaceae
CandglabCandida glabrata CBS 138Saccharomycetaceae
TorudelbTorulaspora delbrueckii NRRL Y-866Saccharomycetaceae