molecular diversity and intragenomic variability in the yeast genus.pdf
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R E S E A R C H A R T I C L E
Molecular diversityand intragenomic variability in the yeast genus
Xanthophyllomyces: the origin ofPhaarhodozyma?
Jack W. Fell1, Gloria Scorzetti1, Adele Statzell-Tallman1 & Kyria Boundy-Mills2
1Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; and 2Phaff Yeast Culture Collection, Food Science
and Technology, University of California Davis, Davis, CA, USA
Correspondence: Jack W. Fell, Rosenstiel
School of Marine and Atmospheric Science,
University of Miami, 4600 Rickenbacker
Causeway, Key Biscayne, FL, USA.
Tel.: 11 305 421 4603; fax:1305 421 4600;
e-mail: [email protected].
Received 28 September 2006; revised 15 June2007; accepted 17 June 2007.
First published online 6 September 2007.
DOI:10.1111/j.1567-1364.2007.00297.x
Editor: Teun Boekhout
Keywords
basidiomycetous yeast; Xanthophyllomyces;
Phaffia; molecular diversity; rRNA gene
sequence analysis; intragenomic sequence
heterogeneity.
Abstract
The teleomorphic basidiomycetous yeast Xanthophyllomyces dendrorhous is im-
portant as a commercial source of astaxanthin, which is a component of feeds for
mariculture. Phaffia rhodozyma is the anamorphic state of Xanthophyllomyces;
however, there are conflicting reports in the literature concerning the presence of a
sexual cycle in P. rhodozyma. The current study attempted to explain this enigma.
Strains were obtained from the Phaff Yeast Culture Collection (University ofCalifornia, Davis) and other sources in the northern hemisphere. Molecular
sequences of three nuclear rDNA regions were examined: the internal transcribed
spacers (ITS), intergenic spacer (IGS1) and the D1D2 region at the 5 0 end of the
26S gene. Different levels of genetic variability were observed in the three regions.
The D1D2 differentiated major groups of strains, while an increased variability in
the ITS suggested that the ITS region could be employed as an ecological marker.
The greatest variability was in the IGS1 region, where strains can be defined by the
presence and location of indels. Intragenomic sequence heterogeneity in the ITS
and IGS1 regions led to the hypothesis that the type strain of P. rhodozyma (CBS
5905T, UCD 67-210T) was derived as a mating-deficient basidiospore from the
parent teleomorphic strain CBS 9090.
Introduction
Phaffia rhodozyma is an economically important basidiomy-
cetous yeast, which is used in commercial feed to produce
pink-colored flesh in salmon and shrimp (Johnson, 2003).
The species was first isolated by Phaff et al. (1972) from
Japan and Alaska and described by Miller et al. (1976) as an
anamorphic species with type strain UCD 67-210T, which
was submitted to the Centraalbureau voor Schimmelcul-
tures as CBS 5905T. Golubev (1995) discovered the tele-
omorphic state based on parentbud mating in strains from
Japan, Finland and Russia. The genus and species were
described as Xanthophyllomyces dendrorhous with the type
strain designated as CBS 7918T.
Golubev (1995) reported that a subculture of the type
strain ofP. rhodozyma (VKM Y-2274T) produced a Xantho-
phyllomyces-type sexual cycle. In contrast, Kucsera et al.
(1998) and research in our laboratory failed to observe a
sexual cycle with strain CBS 5905T. In addition, we obtained
strains, from several laboratories that were labeled UCD 67-
210T or reported to be derived from UCD 67-210T. We
found that some of these strains produced sexual cycles,
whereas other strains lacked that ability. These results
suggested that some strains might be erroneously labeled.
To resolve the confusion, we examined a series of lyophilized
stocks from the years 1968, 1985 and 1986, which are
maintained in the Phaff Yeast Culture Collection at the
University of California at Davis (UCD). The series revealed
two strains that differed on their rRNA gene sequences. One
strain, represented by the 1968 lyophilized stock, was
identical to CBS 5905T. The other strain, represented by the
1985 and 1986 stocks, was unlike previously studied strains
(Fell & Blatt, 1999) and was subsequently labeled UCD 67-
210.2 (CBS 9090, Scorzetti et al., 2002). For comparative
purposes, we included all of the Phaffia/Xanthophyllomyces
strains from the Phaff Collection as well as unstudied strains
in the USDA Collection (NRRL, Peoria, IL; C.P. Kurtzman),
which had been isolated from trees in Illinois and Wiscon-
sin. The studies included observations of sexual cycles,
sequence analyses of nuclear rDNA regions (internal
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transcribed spacers: ITS1 and ITS2, D1D2 region of the large
subunit and the intergenic spacer region 1: IGS1) and
cloning and sequence analysis of ITS and IGS1 regions to
establish the presence of intragenomic sequence heteroge-
neity.
Materials and methods
The strains studied, and the GenBank accession numbers of
their ribosomal sequences, are listed in Table 1. The three
regions examined in the nuclear rDNA were the D1D2
domain at the 5 0 end of the large (26S) subunit (LSU), the
ITS region including ITS1, 5.8S and ITS2 and the IGS1
region, which extends from the LSU to the 5S. Amplification
of the D1D2 and ITS regions was performed with primers
NS7, 50-GAGGCAATAACAGGTCTGTGATGC-3 0, and LR6,
50-CGCCAGTTCTGCTTACC-30. IGS primers were LR11,
50-TTACCACAGGGATAACTGGC-3 0, and 5SR, 5 0-GATC
GGACGGGCAGGGTGC-30. Eppendorf HotMaster Mix
(Eppendorf North America) and DyNAzyme Polymerase
(Finnzymes) were alternatively employed. The optimized
amplification program consisted of one denaturation cycle
at 94 1C for 5 min followed by 35 cycles of 1 min denatura-
tion at 94 1C, 1 min annealing at 551C and 3 min extension
at 72 1C. The final extension was at 72 1C for 7 min. Samples
of the resulting amplicons were analysed by gel electrophor-esis on a 2% agarose minigel. The PCR products were
purified with the QIAquick PCR Purification Kit (Qiagene
Inc.)
The D1D2 domain was sequenced with primers F63,
50-GCATATCAATAAGCGGGAGGAAAAG-30, and (R635)
LR3, 50-GGTCCGTGTTTCAAGACGG-30. The ITS region
was sequenced with primers ITS1, 5 0-TCCGTAGGTGAACC
TGCGG-30, and ITS4, 5 0-TCCTCCGCTTATTGATATGC-30.
The IGS region employed primers LR12, 5 0-CTGAACGCC
TCTAAGTCAGAA-3 0, and 5SR, 50-GATCGGACGGGC
AGGGTGC-30. A LiCor (Lincoln, NB) automated sequencer
with IRD800 conjugate primers was employed for
Table 1. Origin of strains studied
Strain Other numbers Origin
GenBank accession numbers
D1D2 ITS IGS 1
Xanthophyllomyces dendrorhous
ATCC 24228 UCD 68-653.3 Betula papyrifera Alaska DQ870193 AF139631 AF139636
ATCC 24230 UCD 67-385 Betula tauschiiJapan AF139630 AF139635
CBS 6938 VKM Y-2793 Betula sp. Finland AF444793 AF139632 AF13937
CBS 9090 UCD 67-210.2 AF444721 AF444488 DQ870210
CBS 9090 C3 DQ904247
CBS 9090 C4 DQ904243
CBS 9090 C6 DQ904244
CBS 9090 C7 DQ870211
CBS 9090 C10 DQ904245
CBS 7918T T VKM Y-2786 Betula verrucosa Russia AF075496 AF139628
NRRL Y-17430 Betula populifolia Wisconsin DQ870185 DQ870197
NRRL Y-17430 C4
NRRL Y-17431 B. populifolia Wisconsin DQ870186 DQ870198
NRRL Y-17432 B. populifolia Wisconsin DQ870187 DQ870199 DQ870215
NRRL Y-17433 B. populifolia Illinois DQ870188 DQ870200 DQ870216
NRRL Y-17434 B. populifolia Illinois DQ870189 DQ870201 DQ870217
NRRL Y-17434 C1 DQ870218
NRRL Y-17438 B. populifolia Illinois DQ870190 DQ870202 DQ870219
NRRL Y-17438 C2 DQ870220
NRRL Y-17441 B. populifolia Illinois DQ870191 DQ870203 DQ870221
NRRL Y-17441 C9 DQ870222
NRRL Y-17442 B. populifolia Illinois DQ870192 DQ870204 DQ870223
NRRL Y-17443 B. populifolia Illinois DQ913745 DQ913746 DQ913747
NRRL Y-27348 B. populifolia Illinois DQ870205 DQ870224
NRRL Y-27348 C2 DQ870225
UCD 67-202 ATCC 24229 Cornus brachypoda Japan DQ870194 DQ870206
UCD 67-203 ATCC 24201 C. brachypoda Japan DQ870195 DQ870207
Phaffia rhodozyma
CBS 5905T T UCD 67-210T Fagus crenata Japan AF189871 AF139629 AF139634
CBS 5905T C2 DQ904246
CBS 5905T C10 DQ870209
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1400 J.W. Fell et al.
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sequencing. Sequences were analysed with Align IR for Mac
OS 9. The sequences with double pattern images were
resequenced on an ABI 3730 DNA Analyzer (Applied
Biosystems) and analysed with Seqman 5.51 for Mac OS X.
Following amplification and purification, amplicons re-
presenting the IGS1 and ITS regions from selected strains
(Table 1) were ligated and transformed in competent cells(TA Cloning Kit with INVaF chemically competent Escher-
ichia coli, Invitrogen Corp.) using the manufacturers proto-
cols. Sixteen clones from each sample were purified (Wizard
SV 96 Plasmid DNA Purification System, Promega Corp.)
and sequenced with an ABI 3730 DNA Analyzer (Applied
Biosystems) using primers M13F (M13/pUC universal
primer code 1, Sambrook & Russell, 2001) (5 0-GTAAAA
CGACGGCCAGT-30) and M13R (5 0GGAAACAGCTATG
ACCATG30), which is a 3-nt 5 0 extension of M13/pUC
universal primer code 4 (Sambrook & Russell, 2001).
Sequences were analysed with Seqman 5.51 for Mac OS X.
Phylogenetic analysis of the D1D2 region employed max-
imum-likelihood (ML) with the HKY85 substitution model
(Hasegawa et al., 1985) and a heuristic search. The ITS and
IGS analyses compared ML with maximum-parsimony
(MP: gaps treated as missing data) and neighbor-joining
(NJ) analyses. Heuristic search consisted of random step-
wise addition and tree-bisection-reconnection branch swap-
ping (TBR). Bootstrap analyses consisted of 1000 replicates
in a full heuristic search. All analyses employed PAUP 4.0b10.
The MP, ML and NJ analyses agreed in terms of strain
relationships, and therefore the trees illustrated are those
that were considered to be the most appropriate for data
presentation and discussion. The IGS1 region was cloned for
strains CBS 5905T
, 7918T
, 9090, NRRL Y-17430, Y-17431, Y-17432, Y17433, Y-17434, Y-17438, Y-17441 and Y-27348.
Strains cloned for the ITS region were CBS 5905T, 7918T,
9090, Y-17433 and Y-27348. The selection included strains
with and without apparent multiple copies.
Basidial formation was studied with CBS 9090, CBS
5905T and all of the NRRL strains. The strains were grown
for 1 month on 0.5% glucitol yeast nitrogen base (YNB)
agar, then transferred to 0.5% glucitol YNB agar at 18 1C
for 5 days.
Results
D1D2 sequence analysis
Xanthophyllomyces and Phaffia are members of the Cystofi-
lobasidiales (Fig. 1, Fell et al., 1999; Scorzetti et al., 2002),
which includes the teleomorphic genera Mrakia and Cysto-
filobasidium and anamorphic species of the genera Udenio-
myces, Cryptococcus, Itersonilia and Guehomyces. There are
three groups of strains within the Xanthophyllomyces cluster:
(1) all of the X. dendrorhous strains listed in Table 1 have an
identical D1D2 sequence with the exception of CBS 9090,
UCD 67-202 and UCD 67-203; (2) CBS 9090 and P.
rhodozyma (CBS 5905T) have identical sequences, which
differ from CBS 7918T (X. dendrorhous) by the absence of a
T at position 558 (Table 2) and a C instead of a T at position
562; (3) two UCD strains (67-202 and 67-203), as repre-
sented by 67-202, differ from CBS 5905T
and CBS 7918T
bythe presence of a C instead of a T at position 569 (Table 2).
ITS sequence analysis
Analysis of the ITS region (Fig. 2), which includes c. 650bp,
suggests that alignment differences can be related to the
geographic origins of the strains. The two clusters of strains
collected from birch trees (Betula spp.) appear to be closely
related as they differ by a single nucleotide. Greater distances
are demonstrated by the type strain of P. rhodozyma (CBS
5905T), which was obtained from a beech tree (Fagus) and
the UCD strains from dogwood (Cornus brachypoda). The
distinction between CBS 5905T
and CBS 9090 is of particularinterest in this study. As illustrated in Table 3, the majority
of the differences are in the ITS2 region.
IGS1 sequence analysis
There were two major difficulties associated with IGS1
analyses. (1) Some strains demonstrated intragenomic het-
erogeneity between copies of the rDNA operons. This
heterogeneity was indicated by the presence of multiple
patterns in the sequencing images. In some cases, the
secondary patterns were weak and the primary pattern
could be read. In other cases, the strength of the secondary
sequence precluded sequence interpretation. The doublepattern, which initiated in the region of position 390 (Table
4), varied in length from 3040 bp to nearly half of the
sequence. This double pattern corresponded to the most
variable portion of the sequence. As a consequence, not all
strains were included in the IGS1 analysis (Fig. 3, Table 4).
(2) Multiple repeats and indels were present in the se-
quences, which required visual and manual alignments.
Individual strains may have indels at different positions in
the sequence, and therefore alignments varied with the
strains included in the analysis (Table 4).
The IGS1 data consisted of 687 bp. The initial 392 bases
consist of a relatively conserved region, which we examined
with NJ, MP and ML analyses. The first 60 bases from the
primer at the 5 0 end were trimmed due to uneven data
acquisition between strains. The results, as illustrated by an
MP tree (Fig. 3), are similar to the ITS data with the
exception that ATCC24230 and ATCC24228 are on a sepa-
rate branch and CBS 5905T and CBS 9090 have identical
sequences. The greatest sequence diversity is in the 390687
region due to the presence of multiple indels (Table 4). The
number and location of these indels provide markers for
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strain identification. Of particular importance, CBS 9090
and the P. rhodozyma CBS 5905T had identical sequence
alignments with the sole difference based on the presence of
an insertion or deletion at position 482523. Indels, which
were present in all of the strains, were prevalent in a GT-rich
area from 392 to 560 and in a TAC-rich region from 560 to
687. As examples of strain specificity, CBS 7918T is distin-
guished by insertions at 500520 and 560575. Similarly,
Fig. 1. Phylogenetic tree representing nuclear
rDNA D1D2 large subunit sequence analysis of
Cystofilobasidiales prepared by maximum like-
lihood with a heuristic search (PAUP 4.0b10):
4045 rearrangements, tree score 2790. Num-
bers on the branches represent bootstrap
percentages (450%). Cryptococcus
fuscescens, Cryptococcus aerius and
Cryptococcus terricola formed the outgroup.
Table 2. D1D2 Sequence differences between strains of Xanthophyllomyces and Phaffia
Nucleotide position
550 560 570
X. dendrorhous C A G C G C G C C T C T T TA C G G G G T C
UCD 67-202 C A G C G C G C C - C T T C A C G G G G C C
CBS 9090 C A G C G C G C C - C T T C A C G G G G T C
P. rhodozyma C A G C G C G C C - C T T C A C G G G G T C
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NRRL Y17434 and Y 17442 can be separated by a 24-bp
indel in the 603624 TAC region (Table 4).
Cloning experiments
The ITS and IGS regions were cloned to ascertain the
presence of intragenomic sequence heterogeneity, which
was indicated by the double banding pattern in the sequence
images. Strains, with and without a double banding pattern,
were sequenced. Throughout this presentation of results and
discussion, the dominant sequence (as reported to GenBank
and used for tree construction) is signified by the strain
number, i.e. CBS 9090. Clone numbers, such as CBS 9090
C4, designate the sequences obtained from clones.
The ITS cloning experiments did not reveal the presence
of heterogeneity in CBS 7918T, NRRL Y-17433 and Y-27348.
In contrast, clones from CBS 9090 (Fig. 2) had sequences
represented by (1) CBS 9090, (2) CBS 9090 C4, with 2-bp
Fig. 2. Cladogram representing the nuclear
rDNA ITS region of Xanthophyllomyces strains
and clones of CBS9090 (clones C4 and C6) as
prepared by maximum-parsimony analysis with
a heuristic search (PAUP 4.0b10). Midpoint root-
ing (MINF optimization): 2794 rearrangements.
Numbers on branches represent branch lengths.
Numbers in parentheses represent bootstrap
percentages (450%).
Table 3. Partial ITS sequence alignment of CBS 9090 and CBS 5905T
: positions 481660. Lower-case letters indicate nucleotide sequence differences
045184
CBS9090 GAAGCGCGGGCGGTGCCTTGACATGATAAGAAATTGTCGTCGAGtgtcGCTGTCTGTGTG
CBS5905 GAAGCGCGGGCGGTGCCTTGACATGATAAGAAATTGTCGTCGAGC--TGCTGTCTGTGTG
006145
CBS9090 aGTGTGTGggTTTCCTCGGGAAcaCgcaGACTAGCtaGTaCaACTAAaCGACGCATGCGA
CBS5905 TGTGTGTGCTTTTCCTCGGGAAGGCATGGACTAGCCGGTGCGACTAA-CGACGCATGCGA
066106
CBS9090 ACTGCTTCTAACGATACTGTGTGtGtgGtC-TTtGCGGaCtgCaTGCGCACACTTCTGAT
CBS5905 ACTGCTTCTAACGATACTGTGTGGGGAGCCCTTCGCGGGCCCCTTGCGCACACTTCTGAT
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differences from ATCC 24230 and related species and (3)
CBS 9090 C6 (and 9090 C10, Table 1), which was identical to
CBS 5905T. The clones from CBS 5905T were all identical
with one exception. CBS 5905T C2 had the appearance of the
5905x9090 hybrid; however, we conservatively treated the
sequence as a chimera. For reference, the sequence was
submitted to GenBank (Table 1).
Sequencing of the IGS1 clones demonstrated a lack of
intragenomic variability in the IGS1 regions of strains CBS
7918T, NRRL Y17431, Y17432 and Y17433. In contrast, CBS
5905T, Y17430, Y17434, Y17438, Y17441 and Y27348 con-
tained at least two different IGS1 sequences in their
genomes. Analysis of the 60392-bp 5 0 region of the IGS1
(Fig. 3) demonstrated the presence of a limited number of
scattered single nucleotide substitutions. For example (Fig.
3), CBS 5905T C10 and CBS 9090 C7 had two single
nucleotide sequence differences. The other clones were not
included in Fig. 3 due to the apparent lack of significant
substitution differences.
The major differences between clones of a single strain
were in the 392687 region, which contains indels that
represent the gain or loss of repeat units. Table 5 lists the
position of the indels, which can be located in Table 4. For
example, Y-17430 C4, as compared with the dominant
sequence, had an insert (398416) in the GT-rich region
and a deletion (650670) in the TAC region of multiple
repeats (Tables 4 and 5). Y-17434 C1 had two deletions: one
at 432446, the other at 605629. Although the clone study
was limited in numbers of strains analysed, none of the
clones from individual strains was identical to sequences
obtained from other strains. Exceptions were clones ob-
tained from CBS 9090 and CBS 5905T (Table 5, Fig. 3). CBS
5905T C10 had an insert at 482523; as a result, CBS 5905T
C10 was identical to CBS 9090 (with the exception of the
single nucleotide substitution). Clones from CBS 9090 had
three distinct sequences: (1) the dominant CBS 9090 se-
quence; (2) CBS 9090 C7, which had a deletion at 482523,
was identical to CBS 5905T; and (3) CBS 9090 C3, which is
Table 4. Location of indels in the 361-687-bp region of the rDNA IGS1 for strains of Xanthophyllomyces dendrorhous and Phaffia rhodozyma
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not included in Table 5, does not represent a deletion/
insertion event. CBS 9090 C3 (Fig. 3) has the CBS 7918T
type of sequence rather than the 5905T/9090 sequence. The
two types of sequences are distinctly different (Table 4). CBS
9090 C3 aligns with ATCC 24230 with the exception of
differences at four separate base positions (two of the
differences are in the 361687 region, which is not included
in Fig. 3).
Teleomorphic state
The NRRL strains (Table 1) and CBS 9090 formed basidia as
illustrated by Golubev (1998). Previous studies demon-
strated that CBS 6938, ATCC 24230 and UCD 67-202
(ATCC 24229) (Kucsera et al., 1998) also produced sexual
states. CBS 5905T did not produce a sexual stage, either in
our study or the Kucsera et al. (1998) study. Based on
current information, the only known anamorphic strain is
CBS 5905T.
Discussion
The present study was initiated by the conflicting reports
concerning the ability of UCD 67-210T to produce a sexual
cycle. We initially addressed the possibility that a transfer
strain had been mislabeled during the routine maintenance
of the culture collection at UCD. This seemed unlikely
because multiple studies over the years in the UCD labora-
tory had not indicated the presence of additional
Fig. 3. Sequence analysis of nuclear rDNA IGS1
bases 60-392. The cladogram represents rela-
tionships between strains in the 5 0 region pre-
ceding the indels (see Table 3). Clones from CBS
9090 and CBS 5905Tare included in the analysis.
The tree was prepared by maximum-parsimony
analysis (heuristic search) as an unrooted tree
(PAUP 4.0b10). One of two equally parsimonious
trees. Xanthophyllomyces dendrorhousT, type
strain; Phaffia rhodozymaT, type strain. Bases
160 were trimmed due to the lack of completesequence data for some strains. Numbers on
branches represent branch lengths. Numbers in
parentheses represent bootstrap percentages
(450%).
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anamorphic strains in the Phaff Collection. In addition, a
lack of published reports on the isolation of other ana-
morphic strains suggests that the type strain (67-210T) of P.
rhodozyma represents a rare occurrence in nature. To clarify
this point, we sequenced D1D2 and ITS regions of all of the
Phaffia/Xanthophyllomyces strains (16) in the Phaff Collec-
tion (data not shown) and did not find another strain that
resembled 67-210T.
We also investigated the history of the maintenance
transfers of UCD 67-210T. The Phaff Collection has main-
tained a series of lyophilized stocks of UCD 67-210T since
1967. We sequenced subcultures from several of these
transfers and found that the April 1968 stock strain had a
nucleotide sequence identical to that of CBS 5905T
. Inaddition, the April 1968 stock did not produce a sexual
cycle. Of note, a subculture of 67-210T was accessioned in
May 1968 at CBS as CBS 5905T, the designated type strain of
P. rhodozyma. The stocks dated June 1985, July 1985, March
1986 and April 1986 produced a typical Xanthophyllomyces
sexual structure and they had identical IGS and ITS
sequences, which were distinct from CBS 5905T. These
subcultures were identical to strains that had been sent to
us from other laboratories, which we had presumed to be
strains mislabeled as 67-210T. To distinguish the different
strains, the June 1985 transfer stock was designated 67-210.2
and submitted to CBS, where it was accessioned as CBS
9090.
The presence of a teleomorphic strain in the transfer
stocks of 67-210T is possibly the source of the reported
sexual cycle in P. rhodozyma. In particular, Golubev (1995)
reported a sexual cycle in a subculture of the type strain,
which he accessioned as VKM Y-2274T. Golubev (personal
communication) obtained the culture from H.J. Phaff
(UCD) in 1975. Golubevs report of a teleomorphic state
suggests that the VKM strain originated from the same line
as CBS 9090 (UCD 67-210.2) and the apparent strain shift
took place prior to 1975.
This information did not explain the origin of the
teleomorphic strain. As a possible clue to solve this dilem-
ma, we turned our attention to our observations of sequence
heterogeneity. We found that CBS 9090 and CBS 5905T are
heterologous in the ITS and IGS regions. CBS 9090 carriesthe CBS 5905T ITS and IGS sequences and CBS 5905T carries
the CBS 9090 IGS sequence. Other strains of Xanthophyllo-
myces (Table 5) have multiple copies with indel differences,
yet none of these strains had copies that are identical to
other genotypes. Hypothetically, the mating-deficient strain
CBS 5905T (Kucsera et al., 1998) could have originated as a
basidiospore from the parent CBS 9090 strain in the UCD
67-210T culture tube. Conceptually, the detection of a
mating-deficient strain, followed by a teleomorph, does not
correlate with this hypothesis. The anticipation would be to
find the teleomorph, followed by the anamorph. However,
culture purification methods are generally employed in the
course of transfer and submission of subcultures to other
collections. This method entails a streak culture and transfer
of a single colony. By the repeated use of this technique over
time, the anamorphic strain could have been sent to CBS
and subsequently lost in the Phaff Collection to the more
prevalent diploid form.
In conclusion, we hypothesize that the origin of CBS 9090
in the culture collection tube labeled UCD 67-210T was
not the result of a mislabeled strain; rather, strain UCD
67-210T may have been derived from a basidiospore from
the parent teleomorph represented by strain CBS 9090. This
hypothesis could be examined by micromanipulation and
analysis of multiple basidiospores from CBS 9090. In themeantime, researchers should be aware of the heterologous
nature of these strains and that some strains, marked as
UCD 67-210T, represent CBS 9090. The two strains can be
differentiated by ITS sequences (Table 3), either by sequence
analysis or through the use of strain-specific PCR primers or
probes.
In addition to our analysis of the source of these strains,
we gained insight on the use of sequence analysis to
distinguish specific strains (Fell & Blatt, 1999). The genus
Xanthophyllomyces appears to be associated with exudates
from trees, such as birch, beech and dogwood, in temperate
regions throughout the world. The strains isolated from the
different geographic regions demonstrate considerable gen-
otypic variability in the D1D2, ITS and IGS regions.
Although our present comparison is geographically limited,
a greater diversity can be anticipated as the search for new
habitats is expanded. The D1D2 alignments distinguish
three groups (Fig. 1), which are separated by differences at
three positions (Table 1). Additional diversity was recorded
in the ITS region (Fig. 2) with the greatest separation
between the strains isolated from Betula and the strains
Table 5. Location of IGS1 insertions between copies within individual
strains ( sequence repeat is absent, see Table 4)
CBS5905 -------
CBS5905 C10 482523
CBS9090 482523
CBS9090 C7 -------
NRRLY17430 -------, 650670
NRRLY17430 C4 398416, -------
NRRLY17434 432446, 605629
NRRLY17434 C1 -------, -------
NRRLY17438 650670
NRRLY17438 C2 -------
NRRLY17441 604649
NRRLY17441 C9 -------
NRRLY27348 -------
NRRLY27348 C2 420435
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from Fagus and Cornus, which suggests that the ITS region
could be an indicator of host specificity.
Our study viewed ITS variability within the context of
differentiating strains, although many systematic studies
separate species at this level of sequence diversity. For
example, Rhodotorula glutinis and Rhodotorula graminis are
considered to be separate species based on 30% nuclearDNA relatedness, yet they are identical in the ITS region and
differ at one base position in the D1D2. In contrast,
Sporobolomyces holsaticus is a designated synonym of Spor-
idiobolous johnsonii based on 93% relatedness; they are
identical in the D1D2 region and differ by 5 bp in the ITS.
The extensive ITS variability between CBS 5905T and CBS
9090 (30 bp) may not be unusual as mating strains of
Sporidiobolus salmonicolor differ by 26 bp (Scorzetti et al.,
2002). The use of differences in the ITS region to separate
species must be considered on a case-by-case basis: one rule
does not fit all. There are considerable ITS and IGS sequence
differences between strains of Xanthophyllomyces, but at
present, there is no additional biological data (such as
mating genetics) to suggest the presence of more than one
species. The apparent geographic strain isolation provides
an opportunity to explore the state and rate of speciation
within Xanthophyllomyces.
The diversity in the IGS1 region is due to the presence
of indels (Table 4) and differences at specific nucleotide
positions (Fig. 3). The sequence specificity suggests that
these markers could be used in ecology to track the source
and distribution of strains. The method is complicated
by the presence, in some strains, of intragenomic sequence
heterogeneity, which requires cloning to obtain readable
data. Intragenomic variation in the rDNA spacer regionsis not uncommon among fungi and reports include
ITS variation in Fusarium (ODonnell & Cigelnik, 1997)
and IGS variability in hybrids of Cryptococcus neoformans
(Bovers et al., 2006). The sexual state in Xanthophyllomyces
is generally considered to initiate with parentbud mating.
However, Golubev (1995) and Kucsera et al. (1998) reported
mating between independent cells. Consequently, there is
the potential for hybridization between strains. CBS 9090
carries both the 5905T/9090 and 7918T types of sequences in
the ITS and IGS regions. CBS 9090 C4 (ITS) is nearly
identical (3-bp difference) to CBS 7918T (Fig. 2) and CBS
9090 C3 (IGS) aligns with ATCC 24230 (difference of 2 bp,
Fig. 3). However, the distinct tree hosts and geographic
distributions complicate the hypothesis of hybridization.
The potential of sequence heterogeneity caused by poly-
morphisms in the rDNA repeat units could be a more
plausible explanation.
Libkind et al. (2007) reported an extended range of
Xanthophyllomyces to Argentina. The authors isolated
strains from fruiting bodies of the ascomycetes Cyttaria
hariotti, which is a parasite of a southern beech tree,
Nothofagus sp. Based on their ITS analysis, the yeast strains
from Nothofagus represent a separate clade, which is distinct
from clusters representing other tree hosts. Their IGS
analysis indicates that the Nothofagus yeasts are related to
CBS 9090. The Libkind et al. (2007) article appeared while
our manuscript was in revision following journal review.
Consequently, their data were not included in the presentstudy. This extended geographic range and molecular diver-
sity is important for future phylogenetic studies of strains
with consideration of haplotype network analyses (Posada &
Crandall, 2001; Templeton et al., 2005) and of the structures
and evolutionary rates of indels (Mes et al., 2000; Yamane
et al., 2006).
Strains of Phaffia/Xanthophyllomyces are extensively stu-
died and utilized throughout the world. Major corporations
produce astaxanthin for aquaculture, whereas academic
research examines various aspects including the carotenoid
synthesis pathway, culture conditions for improved expres-
sion, and new applications such as colorants for egg yolks
(Johnson, 2003). Clarification of the taxonomic designation
and molecular diversity of the strains can be important for
patent and safety concerns. The present work should assist
researchers in this regard.
Acknowledgements
This study was supported by NSF Grant DEB 0206521. We
gratefully acknowledge C.P. Kurtzman, USDA, Peoria, IL,
for supply of NRRL strains and the laboratory assistance
with mating studies provided by Nicholas Pinel with NSF
REU support. We acknowledge anonymous journal re-viewers, whose comments and questions were instrumental
in the revision of the manuscript.
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