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Generic Concepts in Nectriaceae

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Generic Concepts in Nectriaceae available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 80: 189–245. Generic concepts in Nectriaceae L. Lombard1*, N.A. van der Merwe2, J.Z. Groenewald1, and P.W. Crous1,3,4* 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; 2Department of Genetics, Forestry and Agricultural Biotechnology Centre (FABI), University of Pretoria, Pretoria, 0002, South Africa; 3Forestry and Agricultural Biotechnology Centre (FABI), University of Pretoria, Pretoria, 0002, South Africa; 4Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands *Correspondence: L. Lombard, [email protected]; P.W. Crous, [email protected] Abstract: The ascomycete family Nectriaceae (Hypocreales) includes numerous important plant and human pathogens, as well as several species used extensively in industrial and commercial applications as biodegraders and biocontrol agents. Members of the family are unified by phenotypic characters such as uniloculate ascomata that are yellow, orange-red to purple, and with phialidic asexual morphs. The generic concepts in Nectriaceae are poorly defined, since DNA sequence data have not been available for many of these genera. To address this issue we performed a multi-gene phylogenetic analysis using partial sequences for the 28S large subunit (LSU) nrDNA, the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), the large subunit of the ATP citrate lyase (acl1), the RNA polymerase II largest subunit (rpb1), RNA polymerase II second largest subunit (rpb2), α-actin (act), β-tubulin (tub2), calmodulin (cmdA), histone H3 (his3), and translation elongation factor 1- alpha (tef1) gene regions for available type and authentic strains representing known genera in Nectriaceae, including several genera for which no sequence data were previously available. Supported by morphological observations, the data resolved 47 genera in the Nectriaceae. We re-evaluated the status of several genera, which resulted in the introduction of six new genera to accommodate species that were initially classified based solely on morphological characters. Several generic names are proposed for synonymy based on the abolishment of dual nomenclature. Additionally, a new family is introduced for two genera that were previously accommodated in the Nectriaceae. Key words: Generic concepts, Nectriaceae, Phylogeny, Taxonomy. Taxonomic novelties: New family: Tilachlidiaceae L. Lombard & Crous; New genera: Aquanectria L. Lombard & Crous, Bisifusarium L. Lombard, Crous & W. Gams, Coccinonectria L. Lombard & Crous, Paracremonium L. Lombard & Crous, Rectifusarium L. Lombard, Crous & W. Gams, Xenoacremonium L. Lombard & Crous; New species: Mariannaea humicola L. Lombard & Crous, Neocosmospora rubicola L. Lombard & Crous, Paracremonium inflatum L. Lombard & Crous, P. contagium L. Lombard & Crous, Pseudonectria foliicola L. Lombard & Crous, Rectifusarium robinianum L. Lombard & Crous, Xenoacremonium falcatus L. Lombard & Crous, Xenogliocladiopsis cypellocarpa L. Lombard & Crous; New combinations: Aquanectria penicillioides (Ingold) L. Lombard & Crous, A. submerse (H.J. Huds.) L. Lombard & Crous, Bisifusarium biseptatum (Schroers, Summerbell & O'Donnell) L. Lombard & Crous, B. delphinoides (Schroers, Summerbell, O'Donnell & Lampr.) L. Lombard & Crous, B. dimerum (Penz.) L. Lombard & Crous, B. domesticum (Fr.) L. Lombard & Crous, B. lunatum (Ellis & Everh.) L. Lombard & Crous, B. nectrioides (Wollenw.) L. Lombard & Crous, B. penzigii (Schroers, Summerbell & O'Donnell) L. Lombard & Crous, Calonectria candelabra (Viegas) Rossman, L. Lombard & Crous, C. cylindrospora (Ellis & Everh.) Rossman, L. Lombard & Crous, Clonostachys apocyni (Peck) Rossman, L. Lombard & Crous, C. aurantia (Penz. & Sacc.) Rossman, L. Lombard & Crous, C. blumenaviae (Rehm) Rossman, L. Lombard & Crous, C. gibberosa (Schroers) Rossman, L. Lombard & Crous, C. manihotis (Rick) Rossman, L. Lombard & Crous, C. parva (Schroers) Rossman, L. Lombard & Crous, C. tonduzii (Speg.) Rossman, L. Lombard & Crous, C. tornata (Höhn.) Rossman, L. Lombard & Crous, Coccinonectria pachysandricola (B.O. Dodge) L. Lombard & Crous, C. rusci (Lechat, Gardiennet & J. Fourn.) L. Lombard & Crous, Hydropisphaera fusigera (Berk. & Broome) Rossman, L. Lombard & Crous, Ilyonectria destructans (Zinssm.) Rossman, L. Lombard & Crous, I. macroconidialis (Brayford & Samuels) Rossman, L. Lombard & Crous, Mariannaea catenulatae (Samuels) L. Lombard & Crous, Nectriopsis rexiana (Sacc.) Rossman, L. Lombard & Crous, Neocosmospora ambrosia (Gadd & Loos) L. Lombard & Crous, N. falciformis (Carrion) L. Lombard & Crous, N. illudens (Berk.) L. Lombard & Crous, N. ipomoeae (Halst.) L. Lombard & Crous, N. monilifera (Berk. & Broome) L. Lombard & Crous, N. phaseoli (Burkh.) L. Lombard & Crous, N. plagianthi (Dingley) L. Lombard & Crous, N. ramosa (Bat. & H. Maia) L. Lombard & Crous, N. solani (Mart.) L. Lombard & Crous, N. termitum (Höhn.) L. Lombard & Crous, N. tucumaniae (T. Aoki, O'Donnell, Yos. Homma & Lattanzi) L. Lombard & Crous, N. virguliformis (O'Donnell & T. Aoki) L. Lombard & Crous, Neonectria candida (Ehrenb.) Rossman, L. Lombard & Crous, Penicillifer diparietisporus (J.H. Miller, Giddens & A.A. Foster) Rossman, L. Lombard & Crous, Rectifusarium ventricosum (Appel & Wollenw.) L. Lombard & Crous, Sarcopodium flavolanatum (Berk. & Broome) L. Lombard & Crous, S. mammiforme (Chardon) L. Lombard & Crous, S. oblongisporum (Y. Nong & W.Y. Zhuang) L. Lombard & Crous, S. raripilum (Penz. & Sacc.) L. Lombard & Crous, Sphaerostilbella penicillioides (Corda) Rossman, L. Lombard & Crous, S. aurifila (W.R. Gerard) Rossman, L. Lombard & Crous, Volutella asiana (J. Luo, X.M. Zhang & W.Y. Zhuang) L. Lombard & Crous, Xenoacremonium recifei (Le~ao & L^obo) L. Lombard & Crous; New name: Mariannaea pinicola L. Lombard & Crous; Typification: Epitypification (basionyms): Rectifusarium ventricosum Appel & Wollenw., Xenogliocladiopsis eucalyptorum Crous & W.B. Kendr.. Published online 29 January 2015; http://dx.doi.org/10.1016/j.simyco.2014.12.002. Hard copy: March 2015. INTRODUCTION and are of great importance to agriculture and medicine. They have been extensively exploited in industrial and commercial The order Hypocreales (Hypocreomycetidae, Sordariomycetes, applications (Rossman 1996). These fungi are generally char- Pezizomycotina, Ascomycota) includes approximately 2 700 acterised by the production of lightly to brightly coloured, ostio- fungal species from 240 genera, which are divided over eight late, perithecial ascomata, containing unitunicate asci with families (Kirk et al. 2008, Crous et al. 2014), with some genera hyaline ascospores; asexual morphs, the form most frequently still classified as incertae sedis (Lumbsch & Huhndorf 2007). encountered in nature, are moniliaceous and phialidic (Rogerson Members of this order are globally found in various environments 1970, Samuels & Seifert 1987, Rossman 1996, 2000, Rossman Studies in Mycology Peer review under responsibility of CBS-KNAW Fungal Biodiversity Centre. Copyright © 2014, CBS-KNAW Fungal Biodiversity Centre. Production and hosting by ELSEVIER B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/3.0/). 189 LOMBARD ET AL. et al. 1999). The taxonomic importance of these asexual morphs DNA isolation, amplification and analyses has only been recognised relatively recently (Rossman 2000, Seifert & Samuels 2000). The morphology of asexual forms is Total genomic DNA was extracted from 7-d-old single-conidial often crucial for the morphological identification of these fungi. cultures growing on 2 % (w/v) malt extract agar (MEA) using The family Nectriaceae is characterised by uniloculate the method of Damm et al. (2008). Partial gene sequences were ascomata that are white, yellow, orange-red or purple. These determined for the 28S large subunit (LSU) nrDNA, the internal ascomata change colour in KOH, and are not immersed in a transcribed spacer region and intervening 5.8S nrRNA gene well-developed stroma. They are associated with phialidic (ITS), the large subunit of the ATP citrate lyase (acl1), the RNA asexual morphs producing amerosporous to phragmosporous polymerase II largest subunit (rpb1), RNA polymerase II second conidia (Rossman et al. 1999, Rossman 2000). This family largest subunit (rpb2), β-tubulin (tub2), histone H3 (his3), includes around 55 genera that were originally based on translation elongation factor 1-alpha (tef1), calmodulin (cmdA) asexual or sexual morphs. The genera include approximately and α-actin (act) using the primers and PCR protocols listed in 900 species (www.mycobank.org; www.indexfungorum.org). Table 2. Integrity of the sequences was ensured by sequencing The majority of these species are soil-borne saprobes or weak the amplicons in both directions using the same primer pairs as to virulent, facultative or obligate plant pathogens, while some were used for amplification. A consensus sequence for each are facultatively fungicolous or insecticolous (Rossman et al. locus was assembled in MEGA v. 6 (Tamura et al. 2013) and 1999, Rossman 2000, Chaverri et al. 2011, Gr€afenhan et al. additional sequences were obtained from GenBank (Table 1). 2011, Schroers et al. 2011). Several species have also been Subsequent alignments for each locus were generated in reported as important opportunistic pathogens of humans MAFFT v. 7 (Katoh & Standley 2013) and manually corrected (Chang et al. 2006, de Hoog et al. 2011, Guarro
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