Mycosarcoma (Ustilaginaceae), a resurrected generic name for corn smut (Ustilago maydis) and its close relatives with hypertrophied, tubular sori.

Ustilago is a polyphyletic genus of smut fungi found mainly on Poaceae. The development of a taxonomy that reflects phylogeny requires subdivision of Ustilago into smaller monophyletic genera. Several separate systematic analyses have determined that Macalpinomyces mackinlayi, M. tubiformis, Tolyposporella pachycarpa, Ustilago bouriquetii and U. maydis, occupy a unique phylogenetic position within the Ustilaginaceae. A previously introduced monotypic generic name typified by U. maydis, Mycosarcoma, is available to accommodate these species, which resolves one component of polyphyly for Ustilagos.lat. in Ustilaginaceae. An emended description of Mycosarcoma is provided to reflect the morphological synapomorphies of this monophyletic group. A specimen of Ustilago maydis that has had its genome sequenced is designated as a neotype for this species. Taxonomic stability will further be provided by a forthcoming proposal to conserve the name Uredo maydis over Lycoperdon zeae, which has priority by date, in order to preserve the well-known epithet maydis.

INTRODUCTION

There are 14 genera of smut fungi recognized in Ustilaginaceae (Ustilaginomycetes) on grasses: Anomalomyces, Anthracocystis, Franzpetrakia, Langdonia, Macalpinomyces, Moesziomyces, Sporisorium, Stollia, Tranzscheliella, Triodiomyces, Tubisorus, Ustilago, Yenia, and Yunchangia. These genera are distinguished by morphology of the sori and spores, as well as host range and phylogenetic relationships supported by molecular data (Begerow). Species of Ustilago destroy leaves and inflorescences of hosts in Poaceae, mostly producing sori that rupture at maturity to expose blackish spore masses. Ustilago became a catch-all for many unrelated species of smut fungi, and is polyphyletic (McTaggart, Begerow , Savchenko et al. 2014). Ustilago, in the strict sense, occurs mainly on hosts in the tribe Pooideae and lacks soral structures, specifically, a columella, spore balls and sterile cells (McTaggart ). Additionally, members of the asexual yeast genera Pseudozyma and Farysizyma are polyphyletic in different lineages of Ustilaginales (Begerow , 2014, Boekhout 1995, Inacio , Wang ). Some of these asexual yeasts were described without awareness of their sexual morphs, which are known to be plant pathogenic or potentially plant pathogenic (Wang ). A phylogenetic species concept that places species of yeast into resolved genera has commenced for yeasts in Anthracocystis and other taxa (Piątek , Wang ).

The known genera of smut fungi reflect synapomorphies, whether found in cellular ultrastructure or gross morphological characters of the sorus (Begerow ). These synapomorphies are supported by DNA sequence data (Begerow ). Recent taxonomic changes for smut fungi reflect phylogenetic classification, for example the separation of Microbotryales from Ustilaginomycotina (Begerow , 2014), and division of the Ustilago-Sporisorium-Macalpinomyces complex into smaller, well-defined genera (McTaggart ). In the latter example, smut fungi on grasses in the Ustilago-Sporisorium-Macalpinomyces complex were divided into the genera Anthracocystis, Langdonia, Stollia, Triodiomyces and Tubisorus (Vánky & Lutz 2011, McTaggart ).

Ustilago maydis, the cause of boil or blister smut of corn (Zea mays), forms localized, hypertrophied sori on the stems, leaves and inflorescences. It is an important model organism for the study of reproduction (Bakkeren ), infection pathways (Muller ), virulence and cellular signaling in fungi (Brefort ). It was the first species of Ustilaginomycotina to have a publicly available genome (Kämper ), which has since been used for comparative genomics between corn smut and other fungi (e.g. Xu ). Molecular phylogenetic studies have shown that the mitosporic Pseudozyma prolifica is conspecific with U. maydis (Begerow , Boekhout 2011).

Comparative studies on the genomes of smut fungi have indicated that U. maydis is more closely related to other taxa than to species of Ustilago. For example, differences in the mating systems and methods of RNA silencing between U. maydis and U. hordei (the type species of Ustilago, notwithstanding a proposal by Thines (2016) to conserve Ustilago with U. maydis as the conserved type) indicated a relatively distant phylogenetic relationship (Bakkeren , Bakkeren , Laurie ). Kellner showed the mating type loci of Sporisorium reilianum, Ustanciosporium gigantosporum and related species had some degree of synteny to the corresponding genes of U. maydis. Future studies may determine whether more closely related species have higher synteny and whether genes involved in mating and self-recognition are conserved within genera.

Systematic studies showed that U. maydis was not closely related to species of Ustilago s. str., and was instead recovered as sister to species of Sporisorium and Anthracocystis (Piepenbring , Stoll , Vánky & Lutz 2011, McTaggart ). In these studies, U. maydis was closely related to U. bouriquetii, a smut fungus that forms hypertrophied sori in the inflorescences of Stenotaphrum (Poaceae). McTaggart recovered U. maydis in a clade with Macalpinomyces mackinlayi, M. tubiformis, Tubisorus pachycarpus and U. bouriquetii, which all form hypertrophied sori in inflorescences of their hosts. McTaggart considered that localised, host-derived, hypertrophied sori were an apomorphy for this group (Fig. 2). Vánky & Lutz (2011) introduced a new generic name, Tubisorus, typified by T. pachycarpus, which was recovered in a clade with U. maydis. Tubisorus was characterized by tubular sori filled with spores compacted in loose spore balls.

Fig 2.

A. Mycosarcoma bouriquetii on Stenotaphrum dimidatum (BRIP 26403). B. Mycosarcoma mackinlayi on Eulalia mackinlayi (BRIP 52549). C. Mycosarcoma maydis on Zea mays (BRIP 52746). D. Mycosarcoma tubiforme on Chrysopogon fallax (BRIP 57599).

Mycosarcoma is the earliest available generic name for the clade containing U. maydis, which was described as the type species (Brefeld 1912). The characters that Brefeld (1912) believed distinguished Mycosarcoma from Ustilago and Sporisorium were the: (1) incubation time in the host; (2) development of the sorus at the site of penetration in the host plant; (3) the development of aerial conidia; and (4) the presence of a peridium.

The current systematic understanding of the genera in Ustilaginaceae on Poaceae is shown in (Fig. 1; Table 1). In the present study the circumscription of Mycosarcoma is emended and the name resurrected to reflect contemporary knowledge of the synapomorphies within Ustilaginaceae. A taxonomic system based strictly on morphological synapomorphies is not possible for dimorphic plant pathogenic fungi like U. maydis, which have both asexual non-pathogenic yeast stages and sexual pathogenic teliospore stages in their life cycle.

Fig 1.

Phylogram obtained from a maximum likelihood search in RAxML v8 (Stamatakis 2014) with a partitioned dataset of the internal transcribed spacer and large subunit regions of ribosomal DNA. Bootstrap values (≥70 %) from 1000 replicates in a maximum likelihood search above nodes. Posterior probabilities (≥0.95) summarized from 18 000 converged trees obtained from four runs each consisting of four chains in a Bayesian search with MrBayes (Ronquist & Huelsenbeck 2003) below nodes. GTRGAMMA was the model of evolution for both phylogenetic criteria. Taxon name, host and GenBank numbers listed in Table 1. Type species of the genera included in the Ustilaginaceae are in bold font.

Table 1.

Taxon names and GenBank numbers of isolates used in the phylogenetic analyses.

Taxon	Host	GenBank details
		ITS	LSU
Anomalomyces panici	Panicum trachyrhachis	DQ4593481	DQ4593471
Anthracocystis destruens	Panicum miliaceum	AY3449762	AY7470772
Anthracocystis heteropogonicola	Heteropogon contortus	HQ0131013	HQ0131353
Langdonia aristidae	Aristida hygrometrica	HQ0130963	NA
Langdonia confusa	Aristida queenslandica	HQ0130953	HQ0131323
Langdonia fraseriana	Aristida nitidula	HQ0131003	NA
Macalpinomyces arundinellae-setosae	Arundinella nepalensis	HQ0130863	NA
Macalpinomyces eriachnes	Eriachne aristidea	AY7400372	AY7400902
Macalpinomyces trichopterygis	Trichopteryx dregeana	AY7400392	AY7400922
Macalpinomyces tristachyae	Loudetiopsis chrysothrix	AY7401642	NA
Melanopsichium pennsylvanicum	Polygonum glabrum	AY7400402	AY7400932
Moesziomyces bullatus	Paspalum distichum	AY7401532	AY7401532
Mycosarcoma bouriquetii	Stenotaphrum dimidiatum	AY7401672	NA
Mycosarcoma mackinlayi	Eulalia mackinlayi	GU0148174	HQ0131313
Mycosarcoma maydis	Zea mays	AY3450045	AF4539386
Mycosarcoma pachycarpum	Mnesithea rottboellioides	JN8717187	JN8717177
Mycosarcoma tubiforme	Chrysopogon fallax	HQ0130883	NA
Sporisorium cruentum	Sorghum halepense	AY3449742	AF4539396
Sporisorium reilianum	Zea mays	FJ1673578	DQ8322289
Sporisorium sorghi	Sorghum bicolor	AF03882810	AF00987211
Stollia bursa	Themeda quadrivalvis	AY7401542	NA
Stollia ewartii	Sarga timorensis	HQ0130873	HQ0131273
Triodiomyces altilis	Triodia pungens	AY7401662	HQ0131363
Triodiomyces triodiae	Triodia microstachya	AY7400742	AY7401262
Ustilago avenae	Avena barbata	AY3449975	AF4539336
Ustilago bromivora	Bromus catharticus	AY7400642	AY7401182
Ustilago bullata	Bromus diandrus	AY3449985	AF4539356
Ustilago calamagrostidis	Calamagrostis epigeios	AY7400652	AY7401192
Ustilago cynodontis	Cynodon dactylon	AY3450005	AF00988111
Ustilago davisii	Glyceria multiflora	AY7401692	NA
Ustilago echinata	Phalaris arundinacea	AY3450015	AY7401442
Ustilago hordei	Hordeum vulgare	AY3450035	AF4539436
Ustilago nuda	Hordeum leporinum	AY7400692	JN36733413
Ustilago striiformis	Alopecurus pratensis	AY7401722	DQ87537512
Ustilago tritici	Triticum aestivum	AF13542414	NA
Ustilago vetiveriae	Vetiveria zizanioides	AY3450115	AY7401492

1Vánky ; 2Stoll ; 3McTaggart ; 4McTaggart & Shivas (2009); 5Stoll et al. (2003); 6Piepenbring ; 7Vánky & Lutz (2011); 8Zhang & Gao (unpubl.); 9Matheny ; 10Roux ; 11Begerow ; 12Begerow ; 13Kellner ; and 14Bakkeren .

Vánky (1990) discussed the nomenclatural history of U. maydis. The fungus was first described as Lycoperdon zeae by Beckmann, but this epithet could not be combined in Ustilago as it was pre-occupied by the name U. zeae (Link) Unger 1836 based on a different type (Vánky 1990). The next validly published binomial was U. maydis (DC.) Corda 1842, possibly the most well-known and intensively studied smut fungus in the world. For this reason, we seek to conserve this widely used epithet.

TAXONOMY

The following taxonomic combinations are based on the recovered phylogenetic tree (Fig. 1) and the apomorphies discussed above. Emended parts of the description are in italic type.

Mycosarcoma Bref., Unters. Gesammtgeb. Mykol. 15: 53 (1912).

Description: Sori usually in some ovaries of an inflorescence, derived from hypertrophied host material, often tubular, splitting longitudinally to expose the spore mass, partitioning cells present or absent. Sori rarely in all organs: stems, leaves, inflorescences (male and female) and roots. Columellae absent. Spore balls derived from sporogenous hyphae absent. Germination of the Ustilago-type. Asexual; saprobic stages occur as yeasts on plant surfaces and other habitats.

Hosts: On grass hosts in subfamily Panicoideae (Poaceae).

Type species: Mycosarcoma maydis (DC.) Bref. 1912 (on Zea mays).

Mycosarcoma bouriquetii (Maubl. & Roger) McTaggart, R.G. Shivas & Begerow, comb. nov.

MycoBank MB811941

Basionym: Ustilago bouriquetii Maubl. & Roger, Bull. Soc. Mycol. France 50: 327 (1934).

Synonyms: Sphacelotheca mauritiana Zundel, Mycologia 36: 405 (1944); fide Vánky (1996:107).

Sorosporium stenotaphri Vienn.-Bourg., Ann. Inst. Natl. Agron. 47: 43 (1963); fide Vánky (1996:107).

Type: on Stenotaphrum dimidiatum, Madagascar

Mycosarcoma mackinlayi (McTaggart & R.G. Shivas) McTaggart, R.G. Shivas & Begerow, comb. nov.

MycoBank MB811942

Basionym: Macalpinomyces mackinlayi McTaggart & R.G. Shivas, Persoonia 23: 187 (2009).

Type: on Eulalia mackinlayi, Australia.

Mycosarcoma maydis (DC.) Bref., Unters. Gesammtgeb. Mykol. 15: 53 (1912).

Basionym: Uredo maydis DC., Fl. franç., edn 3, 6: 77 (1815).

Synonyms:Ustilago maydis (DC.) Corda, Icon. Fung. 5: 3 (1842): type: USA: Minnesota: near St Paul, on Zea mays in a corn field, isolated from a germinating teliospore [collected by J.J. Christensen], P. Schreier, R. Kahmann, S. Leong & R. Holiday (DSM 14603 — , MBT374099).

Lycoperdon zeae Beckm., Hannover. Mag. 6: 1330 (1768).

Uredo segetum [var.] mays-zeae DC., Fl. franç., edn 3, 2: 596 (1805).

Ustilago zeae-maydis G. Winter, Rabenh. Krypt.-Fl. 1(1): 97 (1881); as „U. Zeae Mays“.

Ustilago mays-zeae (DC.) Magnus, Verh. Bot. Ver. Prov. Brandenburg 37: 72 (1896) [„1895“].

Uredo zeae Schwein., Schr. Naturf. Ges. Leipzig 1: 71 (1822).

Caeoma zeae Link, Linné’s Sp. Plant., 4 edn, 6(2): 2 (1825).

Ustilago zeae (Link) Unger, Ueber Einfluß Bodens: 211 (1836).

Ustilago euchlaenae Archang., Erb. Crittog. Ital., ser. 2, no. 1152 (1882).

Pseudozyma prolifica Bandoni, Bot. J. Linn. Soc. 91:38 (1985).

Notes: We are proposing elsewhere to the Nomenclature Committee for Fungi (NCF) that the name Uredo maydis should be conserved over Lycoperdon zeae in order to to preserve the well-known epithet “maydis”, which has been used for this species for over two centuries, but does not have priority over “zeae” if combined into Mycosarcoma.

Neither Beckmann (1768) nor de Candolle (1815) designated specimens or illustrations that might serve as the nomenclatural types when Lycoperdon zeae and Uredo maydis were described. Nor were we able to locate specimens in German and French herbaria that pre-dated the descriptions by Beckmann (1768) or de Candolle (1815) that might have been studied by them. As there are no specimens or illustrations associated with the name U. maydis that might serve as a lectotype, we consequently designate a sequenced neotype for Ustilago maydis here. The neotype was chosen on the basis that it represented a typical strain of corn smut with a published genome sequenced by the Broad Institute (Kämper ). Further, populations of corn smut in Europe have been found to be monophyletic (Begerow, unpubl.).

Mycosarcoma pachycarpum (Syd.) McTaggart, R.G. Shivas & Begerow, comb. nov.

MycoBank MB811943

Basionym: Sorosporium pachycarpum Syd., Ann. Mycol. 26: 431 (1928).

Synonyms: Tolyposporella pachycarpa (Syd.) L. Ling, Sydowia 3: 133 (1949).

Endosporisorium pachycarpum (Syd.) Vánky, Mycotaxon 56: 213 (1995).

Tubisorus pachycarpus (Syd.) Vánky & M. Lutz, Mycol. Balcan 8: 131 (2011).

Type: on Rottboellia ophiuroides, Philippines.

Mycosarcoma tubiforme (R.G. Shivas & Vánky) McTaggart, R.G. Shivas & Begerow, comb. nov.

MycoBank MB811944

Basionym: Macalpinomyces tubiformis R.G. Shivas & Vánky, Fung. Divers. 16: 152 (2004).

Type: on Chrysopogon fallax, Australia.

DISCUSSION

Mycosarcoma is resurrected here and the circumscription emended to accommodate a monophyletic group in Ustilaginaceae; this addresses one further component of polyphyly in Ustilago s. lat. This taxonomy is supported by several separate systematic analyses that have determined a unique phylogenetic position of M. maydis within the family (Piepenbring , Stoll , Vánky & Lutz 2011, McTaggart ). We will submit a proposal to the Nomenclature Committee for Fungi for conservation of Uredo maydis over the name Lycoperdon zeae, which has priority at species rank, to avoid a disadvantageous nomenclatural change, as ‘maydis’ is an accepted and widely used epithet for corn smut in plant pathology and genetics. If this proposal is successful, the name M. maydis will become secure.

Future studies that include more taxa and additional phylogenetically informative molecular markers may reveal that other species also belong to Mycosarcoma. In the present study, Macalpinomyces arundinellae-setosae and U. vetiveriae fit the morphological concept of Mycosarcoma, but were not recovered in Mycosarcoma with strong support in the phylogenetic analyses. Detailed studies on the ontogeny of sori and teliospores might help to further clarify the limits of Mycosarcoma. For example, Macalpinomyces trichopterygis, M. tristachyae, and M. simplex, which were included in the phylogenetic analyses, cause systemic infections on grasses in the subfamily Arundinoideae. These three species also have tubular, host-derived sori, and have a phylogenetic affinity with Mycosarcoma as shown in previous studies (Stoll , Vánky & Lutz 2011, McTaggart ).

Thines (2016) proposed that U. maydis should be conserved as the type species of Ustilago to cement the name of this well-studied smut fungus. This was on the grounds that U. hordei, the current type, does not supersede U. segetum, which was designated as lectotype of Ustilago by Clinton (1904). However, U. segetum was not described as a distinct taxon, but initially as a set of three varieties (Persoon 1797), and subsequently sanctioned as a set of five varieties (Persoon 1801), with U. hordei the alpha variety, “Uredo segetum α Uredo hordei”. Most of these varieties were subsequently raised to species rank (Lagerheim 1889, Saccardo 1891), and Clinton (1906) revised the name of his typification to U. hordei (Clinton 1906). As the alpha or ‘typical’ variety, U. hordei represents the name of the type after the species names Ustilago/Reticularia segetum were declared nomina utique rejicienda. Furthermore, Ustilago hordei is a conserved name with a type specimen studied by Persoon.

If Ustilago hordei were not the type, Ustilago maydis would not be a suitable choice as a replacement, because it is not among the species described in the sanctioning work (Art 10.2), it is not congeneric with Ustilago as described by Persoon (1801), and it would require ~200 name changes for species of Ustilago that are not congeneric with U. maydis. The mycological community has previously accepted name changes for model fungi such as Microbotryum violaceum and Zymoseptoria tritici, and the adoption of Mycosarcoma maydis will provide stability for two genera of smut fungi.

Ustilago maydis was recombined in Mycosarcoma a century ago to distinguish it from other species of smut fungi, particularly species of Ustilago. We suggest the scientific community adopts the taxonomy proposed by Brefeld (1912) and summarized here, to ensure classification reflects evolution.