PYCC 2916
1 - Taxon name
Torulaspora delbrueckii
2 - Classification
Ascomycota
3 - Strain (species name) changes
Torula colliculosa; Candida colliculosa; Saccharomyces fermentati
4 - Status of the strain
Type strain of Torula colliculosa
5 - Basis for identification
Molecular (whole genome sequence)
6 - Identified by
Margarida Silva
7 - Original strain number
ISA 1103
8 - Accession numbers in other collections
CBS 133;ATCC 2507;CCRC 21429;IFO 1083;NRRL Y-172
9 - Biological Safety Level
BSL-1
10 - Access and Benefit Sharing (CBD, Nagoya protocol)
No known ABS restrictions
11 - PYCC strain status
Open
12 - Mediterranean strain
No
13 - Substrate of isolation
rhagi
14 - Category of substrate
Food & beverages
15 - Locality
Java
16 - Country of origin
Indonesia
18 - Sample Collected by
NA
19 - Isolated by and date of isolation
NA
20 - Isolation details
NA
21 - Deposited by
CBS 133, 1961
22 - History
CBS > PYCC
23 - Preservation
Glass beads; 20% Glycerol; -150ºC
24 - Price per culture
85€
25 - Remarks
NA
26 - Medium for growth
YMA
DNA Sequence
Region
16S
Sequence Title
X98119
Gene Bank Url
http://www.ncbi.nlm.nih.gov/nuccore/X98119
DNA Sequence
Region
26S
Sequence Title
AJ508558
Gene Bank Url
http://www.ncbi.nlm.nih.gov/nuccore/AJ508558
DNA Sequence
Region
ITS
Sequence Title
AJ224311
Gene Bank Url
http://www.ncbi.nlm.nih.gov/nuccore/AJ224311
DNA Sequence
Region
ITS
Sequence Title
AJ224310
Gene Bank Url
http://www.ncbi.nlm.nih.gov/nuccore/AJ224310
Whole genome
GCA_931301865.1
F1 D-Glucose
+
F2 D-Galactose
-
F3 Maltose
+
F5 Sucrose
+
F6 a,a-Trehalose
-
F7 Melibiose
-
F8 Lactose
-
F9 Cellobiose
-
F10 Melezitose
-
F11 Raffinose
+
F12 Inulin
W, D
C1 D-Glucose
+
C2 D-Galactose
-
C3 L-Sorbose
-
C4 D-Glucosamine
-
C5 D-Ribose
D
C6 D-Xylose
-
C7 L-Arabinose
-
C8 D-Arabinose
-
C9 L-Rhamnose
-
C10 Sucrose
+
C11 Maltose
+
C12 a,a-Trehalose
+
C13 Me a-D-Glucoside
-
C14 Cellobiose
-
C15 Salicin
-
C16 Arbutin spliting
-
C17 Melibiose
-
C18 Lactose
-
C19 Raffinose
+
C20 Melezitose
-
C21 Inulin
+
C22 Starch
-
C23 Glycerol
-
C24 Erythritol
-
C25 Ribitol
-
C28 D-Glucitol
+
C29 D-Mannitol
+
C30 Galactitol
-
C31 myo-Inositol
-
C32 D-Glucono-1,5-lactone
W
C35 D-Gluconate
-
C36 D-Glucuronate
-
C38 DL-Lactate
+
C39 Succinate
-
C40 Citrate
-
C41 Methanol
-
C42 Ethanol
+
C50 L-Malic acid
-
C51 L-Tartaric acid
-
N1 Nitrate
-
N2 Nitrite
W
N3 Ethylamine
+
N4 L-Lysine
+
N5 Cadaverine
-
N6 Creatine
-
N7 Creatinine
-
V1 w/o vitamins
+
O1 Cycloheximide 0.01%
-
O2 Cycloheximide 0.1%
-
O4 50% D-Glucose
+
O6 10% NaCl
W
M1 Starch formation
-
M3 Urea hydrolysis
-
M4 Diazonium Blue B reaction
-
Title
A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast

Author

Margarida Silva, Ana Pontes, Ricardo Franco‐Duarte, Pedro Soares, José Paulo Sampaio, Maria João Sousa, Patrícia H. Brito

Abstract

AbstractMicrobe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked to anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix‐Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix‐Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. In contrast to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread‐production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.

Publication Date

Link to Publication

https://doi.org/10.1111/mec.16428