Urocystis cumminsii sp. nov., a smut fungus on Themidaceae from Arizona

Abstract

The morphology and phylogenetic relationships of a species of Urocystis on Dichelostemma capitatum ( Themidaceae , Asparagales ) collected in the Tucson Mountains in Arizona, United States, were studied using microscopy and ITS rDNA sequence analyses. This is a first record for smut fungi on hosts from Themidaceae. Molecular phylogenetic analyses based on ITS sequence data revealed its basal position in relation to species on Poaceae. As a result, the smut in leaves of Dichelostemma capitatum is described and illustrated here as a new species, Urocystis cumminsii.

Full text

MYCOTAXON
ISSN (print) 0093-4666 (online) 2154-8889 Mycotaxon, Ltd. ©2019
October–December 2019—Volume 134, pp. 591–599
https://doi.org/10.5248/134.591
Urocystis cumminsii sp. nov., a smut fungus
on Themidaceae from Arizona
K G. S*, S R. H,
L M. C, L A. C
1 Department of Biological Sciences, Butler University, Indianapolis, IN 46208
2 Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
3 USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory,
10300 Baltimore Ave, Beltsville, MD 20705, USA
* C : ksavchen@butler.edu
A—e morphology and phylogenetic relationships of a species of Urocy stis on
Dichelostemma capitatum (emidaceae, Asparagales) collected in the Tucson Mountains in
Arizona, United States, were studied using microscopy and ITS rDNA sequence analyses. is
is a rst record for smut fungi on hosts from emidaceae. Molecular phylogenetic analyses
based on ITS sequence data revealed its basal position in relation to species on Poaceae. As
a result, the smut in leaves of Dichelostemma capitatum is described and illustrated here as a
new species, Urocystis cumminsii.
K —plant pathogens, taxonomy Urocystidales
Introduction
Urocystis Rabenh. ex Fuckel contains more than 170 species of plant
pathogenic smut fungi, found all over the world but more common in
temperate areas of both hemispheres (Vánky 2011b). More than 60% of
Urocystis species are found on monocotyledons, with Poaceae serving as a
major monocotyledonous host family, followed by Juncaceae, Hypoxidaceae,
Convallariaceae, Amaryllidaceae, and Hyacinthaceae (Vánky 2011b). e
intra-level phylogenetic relationships of Urocystis species have never been
analysed and thus far only the graminicolous species from triticoid hosts

592 ... Savchenko & al.
T . GenBank sequences used in this study.
S GB . R
Antherospora scillae EF653983 Bauer & al. 2008
A. vaillantii EF653988 Bauer & al. 2008
Urocystis bolivarii KX057771 Savchenko & al. 2017
U. colchici DQ839596 Matheny & al. 2006
U. cumminsii MK575496 is study
U. eranthidis JN367299 Kellner & al. 2011
U. scheri KF668284 Smith & Lutz 2013
U. occulta KX057774, Savchenko & al. 2017
U. trillii HQ239361 Henricot 2010
U. tritici KX057782 Savchenko & al. 2017
Ustilago hordei AY345003 Stoll & al. 2003
Vankya heueri EF667965 Bauer & al. 2008
V. ornithogali EF635910 Bauer & al. 2008
have been included in comprehensive phylogenetic analyses (Savchenko
& al. 2017). Most of the Urocystis species described recently—e.g.,
U. achnatheri L. Guo, U. anemones-narcissiorae Vánky, U. arxanensis
L. Guo, U. beckwithiae Ván k y , U. circaeasteri Vánky, U. dunhuangensis
S.H. He & L. Guo, U. glabella Vánky & R. G. Shivas, U. helanensis L. Guo,
U. koeleriae L. Guo, U. phalaridis Vá n ky, U. puccinelliae L. Guo & H.C.
Zhang, U. rostrariae Piątek, U. sinensis L. Guo, U. skirgielloae Piątek,
U. wangii L. Guo, and U. xilinhotensis L. Guo & H.C. Zhang—were
supported only by morphological and host-specialization data (Guo 2002,
2005, 2006; Guo & Zhang 2004, 2005; He & Guo 2007; Piątek 2006a,
2006b; Vánky 2004, 2005, 2011a; Vánky & Abbasi 2011). e integration
of molecular phylogenetic analyses, host plant taxonomy, and morphology
provides a natural classication for various smut genera (Bauer & al. 2008;
Castlebury & al. 2005; Kruse & al. 2018; Lutz & al. 2008; McTaggart & al.
2012; Savchenko & al. 2013, 2015; Vánky & Lutz 2007), justifying the need
of a phylogenetic study of the genus.
During a survey of Urocystis species diversity in the United States,
we examined a specimen identied as Urocystis sp. on Dichelostemma
capitatum (Benth.) Alph. Wood (emidaceae) from Arizona in the WSP
herbarium. Previously, no Urocystis species had been recorded on hosts
from this family. e present study aimed to resolve the specic status of
the smut on D. capitatum through morphological analysis and determine
its phylogenetic anities within Urocystis.

Urocystis cumminsii sp. nov. (United States) ... 593
Materials & methods
e herbarium specimen is deposited in Washington State University
Mycological Herbarium, Pullman, WA, United States (WSP).
Sorus and spore characteristics were studied using dried herbarium material.
Specimens were examined by light microscopy (LM). Pictures of sori were taken
with a Canon Power Shot G10 camera. For LM, spores were mounted in 90% lactic
acid on a microscope slide, gently heated to boiling point to eliminate air bubbles,
and then examined under a Carl Zeiss Axiostar

light microscope at 1000×
magnication and photographed with a Canon Power Shot G10 camera. At least 50
spore balls were measured, and the variation is presented as a range with extreme
values given in parentheses. Means and standard deviations (SD) are provided aer
the spore size ranges.
For SEM studies, spore balls were attached to metal stubs by double-sided
adhesive tape and coated with gold. Spore surface ornamentation was observed at
15 kV and photographed with a JEOL JSM-6700F scanning electron microscope
with a working distance of c. 12–13 mm.
Sequences from other species of Urocystis and related genera were obtained
from GenBank (T ). Genomic DNA was isolated from spore balls removed
from the herbarium specimen that had been lysed in 1.5 mL tubes for 1 min using
FastPrep®24. Tubes were incubated in a water bath for 5 hours at 55 °C, and DNA
extracted using DNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s
instructions.
DNA was amplied in 20 µl aliquots on an Applied Biosystems® GeneAmp 9700
thermal cycler using ITS1 as the forward primer and ITS4 as the reverse primer
(White & al. 1990).
Standard cycling parameters with an annealing temperature of 57 °C were used
for amplication. PCR products were puried with USB ExoSAP-IT according
to the manufacturer’s instructions, amplied with the forward and reverse PCR
primers with the BigDye® Terminator v3.1 Cycle Sequencing Kit, and sequenced on
an ABI PRISM® 3100 Genetic Analyzer.
Consensus sequences were assembled, aligned, and edited with Geneious 7.1.8
for MacOS and with MAFFT 6.853 (Katoh & al. 2002, Katoh & Toh 2008) using the
L-INS-i option. Maximum Likelihood (ML) was implemented as a search criterion
in RAxML (Stamatakis 2014). GTR+I+G was specied as the evolution model in
MrModeltest (Nylander & al. 2004). e RAxML analyses were run with a rapid
Bootstrap analysis (command –f a) using a random starting tree and 1000 maximum
likelihood bootstrap replicates. A Markov Chain Monte Carlo (MCMC) search in
a Bayesian analysis (BA) was conducted with MrBayes (Ronquist & Huelsenbeck
2003). Four runs were implemented for 5 million generations. e cold chain was
heated to a temperature of 0.25°C. Substitution model parameters were sampled
every 500 generations and trees were saved every 1000 generations. Convergence
of the Bayesian analysis was conrmed using AWTY (Nylander & al. 2008) and a

594 ... Savchenko & al.
F. . Bayesian inference of phylogenetic relationships resulting from the analysis of ITS
nucleotide sequence data. Numbers on branches are estimates for PPs from Bayesian inference
(only probabilities >0.8 are shown).
burn-in of 18,000 generations was calculated. e ML and Bayesian analyses were
run three times to test accuracy. e tree was rooted using Ustilago hordei (Pers.)
Lagerh.
Results
e ITS alignment of 13 sequences (including the outgroup Ustilago hordei)
comprised 643 characters including gaps. e dierent BA and ML analytical
runs yielded consistent topologies in respect to well-supported branches
(a posteriori probability >90% in most cases). e consensus tree of one run of
Bayesian phylogenetic analyses is presented in F. 1. e Urocystis sequences
fell into two major clades. e rst clade comprised species from Poaceae and
emidaceae, and the second clade included species from Cyperaceae, Liliaceae
s.l., and Ranunculaceae. e two species from the genus Vankya Ershad
clustered together with the second Urocystis clade.

Urocystis cumminsii sp. nov. (United States) ... 595
F. . Urocystis cumminsii (WSP 68198). A. sori in leaves of Dichelostemma capitatum; B. spore
balls seen by SEM; C, D. spore balls seen by LM. Scale bars: A = 2 mm, B = 5 µm, C, D = 20 µm.
Taxonomy
Urocystis cumminsii K.G. Savchenko, Carris & Castl., sp. nov. F. 
MB 
Diers from Urocystis camassiae by its lighter colored yellowish-brown spores with
thicker walls and its smaller thinner walled sterile cells, and by its host specialization
on emidaceae.
T: USA. Arizona, King’s Canyon, 16 km west of Tucson, on Dichelostemma capitatum
(as D. pulchellum), 30.03.1981, leg. G.B. Cummins (Holotype, WSP 68198; GenBank
MK575496).
E: Named aer George B. Cummins (1904–2007), an eminent American
mycologist, who collected the holotype specimen.

596 ... Savchenko & al.
S in leaves as slightly elevated, pustular, elongate areas of various size and
shape, sometimes conuent, visible on both sides of the leaf, initially lead-
colored and covered by the epidermis which ruptures exposing the powdery,
black mass of spore balls. S  globose, subglobose, ovoid to irregular,
20–45 µm diam., composed of 1–6 (mostly 3) spores and more or less complete
investing layer of sterile cells. S subglobose, ovoid, irregularly oblong to
elongated,
11–15 × 12–18 µm diam. [mean ± SD, 13.3 ± 2.6 × 15 ± 2.9 µm]
,
medium yellowish brown, wall 1–1.5 µm thick, smooth. S 
subglobose, elongated, ovoid, 5–7 × 5–11(–13) µm, pale yellow, to almost
hyaline, with smooth, 1 µm thick wall.
Discussion
Dichelostemma Kunth is a North American genus of wild hyacinths, closely
related to Brodiaea Sm., from the family emidaceae. Plants from this family
are native to Central America and western North America, from British
Columbia to Guatemala (Pires & Sytsma 2002, Stevens 2018). No members of
emidaceae were previously known to be parasitized by smut fungi (Vánky
2011b). Our molecular phylogenetic analyses and morphological data have
helped resolve the systematic position of Urocystis on D. capitatum.
e only possible close relative to U. cumminsii might be another native
North American species, U. camassiae Vá n k y, found on Camassia Lindl.
(Agavaceae; Fay & Chase 1996, Pires & Sytsma 2002). However, U. camassiae
is distinguished by its darker colored reddish-brown spores with thinner spore
walls (0.5–1 µm) and its larger (5–17 µm) sterile cells with thicker walls (1–2
(–3) µm; Vánky 1994).
ITS phylogenetic analysis infers that U. cumminsii is sister to the clade of
Urocystis species on grasses and separate from species found on hosts from
families more closely related to emidaceae, such as U. colchici (Schltdl.)
Rabenh. ex A.A. Fisch. Waldh. and U. trillii H.S. Jacks., indicating multiple
inter-family host jumps during the evolution of Urocystis species, similar to
those in the closely related genus ecaphora Fingerh. (Vasighzadeh & al.
2014). Interestingly, Vankya heueri (Fuckel) Ershad and V. ornithogali (J.C.
Schmidt & Kunze) Ershad also clustered within the Urocystis lineage (F. ).
Most sequences of Urocystis in GenBank are derived from the LSU region.
Unfortunately, our preliminary analysis showed that LSU is not informative for
Urocystis phylogenetics. Hence, we based our current phylogeny on ITS data,
utilizing the limited number of Urocystis ITS sequences available in GenBank.
Additional sequencing is needed to resolve the taxonomy and evolutionary

Urocystis cumminsii sp. nov. (United States) ... 597
relationships within Urocystis, as well as the phylogenetic aliation of closely
related genera, such as Vankya.
Urocystis cumminsii expands the occurrence of Urocystis species to the
host family emidaceae. Future combined molecular phylogenetic and
morphological analyses may reveal higher diversity among Urocystis species in
North America.
Acknowledgments
e authors are grateful to Mary Catherine Aime (Purdue University, Lafayette IN,
U.S.A.) and Marcin Piątek (W. Szafer Institute of Botany, Polish Academy of Sciences,
Krakow) for peer reviewing the manuscript and Shaun Pennycook for his valuable
comments. Funding for this work was provided by USDA-APHIS 2017 Farm Bill
Projects 3.0245.01 and 3.0245.02.
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