Ustilago

Ustilago

 

Background

Ustilago is the largest genus of the Ustilaginaceae in the order of smut fungi, Ustilaginales, with about 200 currently accepted species (Vánky 2013). Ustilago and related genera contain many important plant pathogens that destroy the inflorescence or culms of grasses (Poaceae) (Vánky 2011). Some agriculturally important pathogens of grain and edible crops are U. tritici on wheat (Triticum), U. hordei on barley (Hordeum) and U. maydis on corn (Zea mays). Species of Ustilago have been used as model organisms for the study of plant disease pathways and mating types (Andrews et 2000; Bakkeren et al. 2008; Kellner et al. 2011), as well as for studies in the co-evolution of pathogens with their hosts (Begerow et al. 2004). The genomes of U. maydis and U. hordei were released in 2003 and 2012, respectively (Kamper et al. 2006; Laurie et al. 2012). Ustilago was until recently a catch-all genus for smut fungi on a diversity of host families, including the Carophyllaceae, Cyperaceae, Poaceae, Polygonaceae, Restionaceae, and Tilliaceae (McTaggart et al. 2012b). Closely related genera were not easily distinguished from Ustilago by morphology and formed a complex (Stoll et al. 2003, 2005). Subsequent systematic studies reserved Ustilago s. lat.  for species that infected Poaceae, with Ustilago s. str. restricted to the tribe Pooideae (McTaggart et al. 2012a; Stoll et al. 2005). Soral morphology and host range were later found to be synapomorphic character states for the smut genera Anthracocystis, Langdonia, Sporisorium, Stollia, and Triodiomyces, which were differentiated from Ustilago (McTaggart et al. 2012c). Melanopsichium is closely related to Ustilago and appears to have jumped hosts from Poaceae to Polygonaceae (Begerow et al.  2004; Stoll et al. 2005).

 

Species identification and numbers

The diversity of smuts in the Ustilaginaceae on Poaceae encompasses over 530 species (Vánky 2011). Cryptic species are certain to be revealed when species complexes, e.g., Macalpinomyces eriachnes, are investigated. Vánky (2011) recognized approximately 170 species of Ustilago, which were delimited by host and spore morphology. It is likely the species number of Ustilago will decrease when generic concepts are resolved in the Ustilaginaceae. Species currently recognized as Ustilago will be transferred to new or other genera delimited by sorus morphology and host range. For example, U. maydis does not fit the concept of Ustilago s. str. and warrants transfer to the earliest valid genus, Mycosarcoma, when these closely related genera are resolved (McTaggart et al. 2012a; Stoll et al. 2005; Vánky and Lutz 2011; Piepenbring et al. 2002) (Table).

Table Ustilago. Details of the isolates used in the phylogenetic tree

Species

 

Isolate Host Marker/GenBank accession no.
ITS LSU
Anomalomyces panici BRIP 46421 Panicum trachyrachis DQ459348 DQ459347
Anthracocystis destruens Ust. Exs. 472 Panicum miliaceum AY344976 AY747077
Langdonia aristidae BRIP 52755 Aristida hygrometrica HQ013096 NA
Macalpinomyces eriachnes 56573 (M) Eriachne aristidea AY740037 AY740090
M. mackinlayi BRIP 52549 Eulalia mackinlayi GU014817 HQ013131
M. neglectus RB 2056 (TUB) Setaria pumila AY740056 AY740109
M. simplex 56577 (M) Loudetia simplex AY740152 NA
M. spermophorus HUV 13634 Eragrostis ferruginea AY740171 NA
  BRIP 51858 Sporobolus australasicus NA HQ013130
M. viridans BRIP 49133 Sporobolus actinocladus HQ013089 HQ013125
Melanopsichium pennsylvanicum HUV 17548 Polygonum glabrum AY740040 AY740093
Moesziomyces bullatus Ust. Exs. 833 Paspalum distichum AY740153 AY740153
Sporisorium aegyptiacum Ust. Exs. 756 Schismus arabicus AY344970 AY740129
S. sorghi MP 2036a (USJ) Sorgum bicolor AY740021 AF009872
S. spinulosum HMAS 193085 Capillipedium parviflorum GU139172 GU139171
Stollia ewartii BRIP 51818 Sarga timorense HQ013087 HQ013127
Triodiomyces altilis Ust. Exs. 418 Triodia pungens AY740166 NA
  BRIP 52543 Triodia sp. NA HQ013136
T. triodiae HUV 17662 Triodia microstachya AY740074 AY740126
Tubisorus pachycarpus HUV 21891 Mnesithea rottboellioides JN871718 JN871717
Ustilago affinis MP 692 Stenotaphrum secundatum AY344995 AF133581
U. austro-africana 56516 (M) Enneapogon cenchroides AY740061 AY740115
U. avenae DB 559 (TUB) Avena barbata AY344997 AF453933
U. bouriqueti 56517 (M) Stenotaphrum dimidiatum AY740167 NA
U. bromivora HUV 19322 Bromus catharticus AY740064 AY740118
U. bullata MP 2363 (TUB) Bromus diandrus AY344998 AF453935
U. calamagrostidis 56518 (M) Calamagrostis epigeios AY740065 AY740119
U. crameri Ust. Exs. 995 Setaria italica AY344999 AY740143
U. curta Ust. Exs. 1090 Tripogon loliiformis AY740165 HQ013123
U. cynodontis MP 1838 Cynodon dactylon AY345000 AF009881
U. davisii HUV 19252 Glyceria multiflora AY740169 NA
U. drakensbergiana 56523 (M) Digitaria tricholaenoides AY740170  
U. echinata Ust. Exs. 540 Phalaris arundinacea AY345001 AY740144
U. esculenta Ust. Exs. 590 Zizania latifolia AY345002 AF453937
U. filiformis RB 3011 (TUB) Glyceria fluitans AY740066 AY740120
U. hordei Ust. Exs. 784 Hordeum vulgare AY345003 AF453943
U. ixophori MP 2194 Ixophorus unisetus AY740067 AY740121
U. maydis RB 3093 Zea mays AY345004 NA
  NA Zea mays NA AF453938
U. nuda HUV 17782 Hordeum leporinum AY740069 AJ236139
U. pamirica Ust. Exs. 789 Bromus gracillimus AY345005 AY740145
U. schmidtiae BRIP 51848 Enneapogon sp. HQ013121 HQ013129
U. schroeteriana Ust. Exs. 887 Paspalum paniculatum AY345006 AY740146
U. sparsa Ust. Exs. 892 Dactyloctenium radulans AY345008 NA
U. sporoboli-indici BRIP 39706 Sporobolous pyramidalis AY772736 NA
U. striiformis HUV 18286 Alopecurus pratensis AY740172 DQ875375
U. syntherismae Ust. Exs. 998 Digitaria ternata AY740071 AY740123
U. tragana 56562 (M) Tragus berteronianus AY7400723 AY7401243
U. tritici NA Triticum aestivum AF13542411 NA
U. trichophora 56564 (M) Echinochloa colona AY3450093 AY7401483
U. turcomanica HUV 23 Eremopyrum distans AY3450113 AF4539363
U. vetiveriae HUV 17954 Vetiveria zizanioides AY3450113 AF4539373
U. xerochloae Ust. Exs. 1000 Xerochloa imberbis AY3450123 AF4539383

Ex-type (ex-epitype) strains are bolded and marked with an * and voucher stains are bolded

 

Molecular phylogeny

Relationships between Ustilago and closely related genera are still unresolved, and Ustilago is polyphyletic (Fig. Ustilago). Systematic studies based on the nLSU or ITS regions of rDNA have assigned taxa within these closely related genera (Shivas et al. 2013a; Vánky and Lutz 2011; McTaggart et al. 2012c). Nuclear genes (EF1α, GPDH, RPB1, and RPB2), another ribosomal gene (SSU) and mating loci were explored as markers for the evolution of smut fungi in the Ustilaginaceae (Kellner et al. 2011; McTaggart et al. 2012a; Munkacsi et al. 2007). At this stage, these markers are not as widely used as ITS and LSU, which are recommended for species identification and generic placement, respectively.

Fig. Phylogram generated from ML search in RA×ML based on combined ITS and LSU sequenced data of Ustilago. Bootstrap support values greater than 70 % are indicated above the nodes. The ex-type (ex-epitype) and voucher strains are in bold

 

Recommended genetic markers

  • The large subunit (LSU) of nrDNA–generic level
  • The internal transcribed spacer (ITS) of nrDNA–species level

 

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