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Phylogeny of the Kickxellomycotina and other fungal taxa based on an alignment of MCM7 translated protein sequences. Tree is based on a 50 % majority-rules consensus of 10k trees produced with Bayesian inference (5k used as burn-in). Numbers above branches are Bayesian posterior probabilities. Numbers below branches are maximum-likelihood bootstrap supports produced from 100 bootstrap replicates. Bold branches are highly supported (> 95 % BPP and > .70 MLBP).
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The recently recognised protein-coding genes MCM7 and TSR1 have shown significant promise for phylogenetic resolution within the Ascomycota and Basidiomycota, but have remained unexamined within other fungal groups (except for Mucorales). We designed and tested primers to amplify these genes across early-diverging fungal clades, with emphasis on th...
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... total of nine topologies were produced by our analyses ( Fig. 1-5 and S1-S4). Six of the analyses used a large number of taxa (76 -81) and were primarily intended to investigate the use of MCM7, whereas three of the analyses used a smaller number (38)(39) and were intended to evaluate the use of TSR1 and the combined four-gene analysis (see Table 2). For all of the analyses, branches were ...
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... analysis (noting also the differences in taxon number between them). Since this, along with Wang (2012), represent the first multi-gene studies primarily concentrating on the Kickxellomy cotina that includes sequences from both rDNA and protein- coding genes, we also present a clade-based phylogenetic perspective on the various clades presented (Fig. ...
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... sampling). However, existing analyses do offer hints. James et al. (2006a) used a combination of three rDNA genes and three protein-coding genes to place the Entomophthoromy cotina, Kickxellomycotina and Zoopagomycotina on an unsup- ported branch along with the Dikarya, the Glomeromycota, and the Mucoromycotina. However, our MCM7 protein tree (Fig. 1) placed the Entomophthoromycotina, the Kickxellomycotina and the Zoopagomycotina in a group together with Blastocladiomy cota, and separate from the Dikarya and the Mucoromycotina. That branch was supported by the Bayesian but not by the maximum-likelihood analysis (BPP: 98.3 %, MLBP: 37/100). The four-gene tree (Fig. 5) placed ...
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... regard to the later-diverging fungi, the TSR1 protein tree (Fig. 2) placed the Dikarya on a well-supported branch (BPP: 100.0 %, MLBP: 70/100). The MCM7 protein tree (Fig. 1) placed the Ascomycota together with the Mucoromycotina, but was not well supported (BPP: 69.1 %, MLBP: 40/100). Multi-gene analy- ses (Fig. 4, 5) recovered a well-supported Dikarya ...
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... MCM7 protein tree ( Fig. 1) recovered a monophyletic Kickxellomycotina with seven major subclades (BPP: 100.0 %, MLBP: 86/100). These included three of the four known orders; Dimargaritales, Harpellales and Kickxellales, and four genera, Barbatospora, Orphella, Ramicandelaber and Spiromyces, likely to represent new orders (in a subsequent publication). The TSR1 ...
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... trees presented a branch that contained all members of the orders Harpellales and Kickxellales except for the genus Rami candelaber. This branch was well supported in both the MCM7 ( Fig. 1; BPP: 99.9 %, MLBP: 74/100) and TSR1 ( This strongly suggests that the Harpellales and Kickxellales (except for Ramicandelaber) form a monophyletic group, and Ramicandelaber may not be closely related to the Kickxellales. Within this group, no tree (in which they are present) places the genera Barbatospora or Orphella in a monophyletic ...
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... TSR1 analysis of the Harpellales (Fig. 2) does not fully agree with the phylogeny provided by the MCM7 protein or rDNA tree ( Fig. 1, 3). Although a monophyletic Harpellales was obtained, the topology within the group is not completely congruent with the other analyses, or analyses using RPB1 and RPB2 (not shown, White et al. unpubl. data). TSR1 presented difficulties from aligning the nucleotide sequences to identifying and removing introns, and finally in aligning ...
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... the monophyletic Kickxellales, relationships are difficult to resolve. The group consisting of Coemansia braziliensis, Coemansia reversa and Spirodactylon aureum was first shown by O' Donnell et al. (1998) and again by White et al. (2006a). This relationship is further demonstrated by both the MCM7 ( Fig. 1; BPP: 98.2 %, MLBP: 75/100) and TSR1 phylogenies ( Fig. 2; BPP: 100.0 %, MLBP: 100/100), providing multi-gene support. However, in both the MCM7 ( Fig. 1; BPP: 100.0 %, MLBP: 100/100) and TSR1 ( Fig. 2; BPP: 100.0 %, MLBP: 100/100) analyses, C. reversa and C. braziliensis are placed together, while in the rDNA analysis (as for the ...
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... Coemansia reversa and Spirodactylon aureum was first shown by O' Donnell et al. (1998) and again by White et al. (2006a). This relationship is further demonstrated by both the MCM7 ( Fig. 1; BPP: 98.2 %, MLBP: 75/100) and TSR1 phylogenies ( Fig. 2; BPP: 100.0 %, MLBP: 100/100), providing multi-gene support. However, in both the MCM7 ( Fig. 1; BPP: 100.0 %, MLBP: 100/100) and TSR1 ( Fig. 2; BPP: 100.0 %, MLBP: 100/100) analyses, C. reversa and C. braziliensis are placed together, while in the rDNA analysis (as for the previous pub- lished analyses, which also utilised rDNA) C. reversa is placed together with S. aureum, which renders Coemansia polyphyletic ( Fig. 3; BPP: ...
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... relationships between the members of the Kickxellales are more difficult to resolve. Both the MCM7 and TSR1 indi- vidual gene trees ( Fig. 1, 2) are not well resolved within the Kickxellales clade. The 3-gene tree (Fig. 4) is well resolved with regard to internal members of the group; a poorly-supported group consisting of Dipsacomyces and Martensiomyces is the most early-diverging member (BPP: 86.5 %, MLBP: not pre- sent), followed by well-supported individual branches ...
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... analysis (Fig. 5), however, does not strongly support these internal branches (possibly due to contrasting signal from TSR1), but does strongly support the relationship between Dipsacomyces and Martensiomyces (BPP: 100.0 %, MLBP: 83/100). This relationship is present, although not as strongly supported, in all four individual-gene analyses ( Fig. 1, 2, S2, S3) as well as previously by O'Donnell et al. ...
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... Kickxellales, Orphella and Spiromyces are together on a strongly-supported branch within the TSR1 ( Fig. 2; BPP: 100.0 %, MLBP: 75/100), rDNA ( Fig. 3; BPP: 100.0 %, MLBP: 90/100), 3-gene ( Fig. 4; BPP: 99.9 %, MLBP: 91/100), and 4-gene analyses ( Fig. 5; BPP: 100.0 %, MLBP: 95/100), and a branch that is not strongly supported within the MCM7 ( Fig. 1; BPP: 86.4 %, MLBP: 48/100) analysis. The position of Barbatospora, which is one of the most consistent and well supported evolutionary hypotheses provided by this study, may suggest that the species is an 'offshoot' from an ancestral clade that split to form the Kickxellales and Harpel lales. Thus, Barbatospora might offer valuable ...
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... collar regions of the generative cells of Harpellales ( Moss & Young 1978). It is also one of the few Kickxellales that is dry-spored at maturity. Spiromyces species are saprobic and usually associ- ated with dung. We were able to amplify and sequence both MCM7 and TSR1 for Spiromyces, but neither single-gene tree is able to place it reliably ( Fig. 1, 2). Within the 3-gene tree (Fig. 4), Spiromyces is placed as a sister clade to a group consisting of the Kickxellales (except Ramicandelaber) and Orphella (BPP: 100.0 %, MLBP: 88/100). Within the 4-gene tree (Fig. 5), Spiro myces is with the Kickxellales (except Ramicandelaber) as the earliest-diverging member (but recall Orphella is ...
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... branches (Benny 2005). It is also unusual how, in age, Ramicandelaber sporocladia broaden and become covered with more pseudo- phialides, which become subspherical ( Ogawa et al. 2001). Previous molecular studies have placed Ramicandelaber apart from the Harpellales andKickxellales (Ogawa et al. 2005, White et al. 2006a). On the MCM7 tree ( Fig. 1), Ramicandelaber is placed within the Kickxellomycotina on an early-diverging branch along with Dimargaris (note however that this branch was only supported by the Bayesian analysis; BPP: 97.5 %, MLBP: 59/100). Within the TSR1 analysis (Fig. 2), it was placed as an unsupported branch as the earliest-diverging member of the ...
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... BPP: 97.5 %, MLBP: 59/100). Within the TSR1 analysis (Fig. 2), it was placed as an unsupported branch as the earliest-diverging member of the Kickxellomycotina (recall that the Dimargaritales sample was not placed correctly on this tree due to amplification of the fungal host of Dimargaris; BPP: 85 %, MLBP: 40/100). Within all five analyses ( Fig. 1-5) Ramicandelaber is placed outside of a well-supported clade that contains all other members of the Kickxellales and the Harpellales (except, in the case of the rDNA analysis, Barbatospora). These results suggest that the rDNA-based placement of Ramicandelaber outside of the Kickxellales is likely an accurate one, and that this genus ...
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... in some studies (Tanabe et al., 2005;Tretter et al., 2013). This placement was shown to be caused by high evolutionary rates in certain genera in the Zoopagomycota. ...
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The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.
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Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives ( Mucor circinelloides complex – MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1 , tsr1 , mcm7 , and cfs , introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides , M. griseocyanus, M. janssenii, M. lusitanicus , M. ramosissimus, M. variicolumellatus , and M. velutinosus .
... A review of the literature highlighted genes worthy of detailed investigation in the PMs. This shortlist includes actin (McElroy et al. 1990;Reece et al. 1992;Baldauf et al. 2000;Wöstemeyer 2000, 2001;Daniel et al. 2001;Daniel and Meyer 2003;Yun et al. 2003;Opalski et al. 2005;Hunter et al. 2006), βtubulin (O'Donnell et al. 1998bde Jong et al. 2001;McKean et al. 2001;Einax and Voigt 2003;Juuti et al. 2005), calmodulin (Stevens 1983;O'Donnell et al. 2000;Mulè et al. 2004;Wang and Zhuang 2007;Madrid et al. 2009;Romeo et al. 2011;Samson et al. 2014), chitin synthase (Chs) (Roberts et al. 1986;Debono and Gordee 1994;Kano et al. 1997;Zhang et al. 2000;Kong et al. 2012), elongation factor 1 alpha (EF1-α) (O'Donnell et al. 1998a;Roger et al. 1999;Baldauf et al. 2000;Seifert and Lévesque 2004;Kristensen et al. 2005;Hunter et al. 2006;Maphosa et al. 2006;Matheny et al. 2007;Amatulli et al. 2010), Mcm7 (Moir et al. 1982Kearsey and Labib 1998;Aguileta et al. 2008;Schmitt et al. 2009;Leavitt et al. 2011;Raja et al. 2011;Divakar et al. 2012;Morgenstern et al. 2012;Minnis and Lindner 2013;Tretter et al. 2013Tretter et al. , 2014Prieto and Wedin 2016), and Tsr1 (Gelperin et al. 2001;Schmitt et al. 2009;Tretter et al. 2013;Sadowska-Deś et al. 2013). In the present study, the possibility of developing working molecular markers for these regions for PM samples collected through a citizen science survey in the UK was investigated. ...
... A review of the literature highlighted genes worthy of detailed investigation in the PMs. This shortlist includes actin (McElroy et al. 1990;Reece et al. 1992;Baldauf et al. 2000;Wöstemeyer 2000, 2001;Daniel et al. 2001;Daniel and Meyer 2003;Yun et al. 2003;Opalski et al. 2005;Hunter et al. 2006), βtubulin (O'Donnell et al. 1998bde Jong et al. 2001;McKean et al. 2001;Einax and Voigt 2003;Juuti et al. 2005), calmodulin (Stevens 1983;O'Donnell et al. 2000;Mulè et al. 2004;Wang and Zhuang 2007;Madrid et al. 2009;Romeo et al. 2011;Samson et al. 2014), chitin synthase (Chs) (Roberts et al. 1986;Debono and Gordee 1994;Kano et al. 1997;Zhang et al. 2000;Kong et al. 2012), elongation factor 1 alpha (EF1-α) (O'Donnell et al. 1998a;Roger et al. 1999;Baldauf et al. 2000;Seifert and Lévesque 2004;Kristensen et al. 2005;Hunter et al. 2006;Maphosa et al. 2006;Matheny et al. 2007;Amatulli et al. 2010), Mcm7 (Moir et al. 1982Kearsey and Labib 1998;Aguileta et al. 2008;Schmitt et al. 2009;Leavitt et al. 2011;Raja et al. 2011;Divakar et al. 2012;Morgenstern et al. 2012;Minnis and Lindner 2013;Tretter et al. 2013Tretter et al. , 2014Prieto and Wedin 2016), and Tsr1 (Gelperin et al. 2001;Schmitt et al. 2009;Tretter et al. 2013;Sadowska-Deś et al. 2013). In the present study, the possibility of developing working molecular markers for these regions for PM samples collected through a citizen science survey in the UK was investigated. ...
... The actin gene in particular has received both positive (Baldauf et al. 2000;Wöstemeyer 2000, 2001;Daniel et al. 2001;Daniel and Meyer 2003) and negative (Weiland and Sundsbak 2000;Hunter et al. 2006) reviews. In contrast, the few studies to have used Tsr1 have been mostly positive (Schmitt et al. 2009;Sadowska-Deś et al. 2013;Tretter et al. 2013); however, as in the present study, it was not considered to offer sufficient resolution in the study of Morgenstern et al. (2012). β-tubulin has regularly emerged as a strong candidate for complementing the ITS in fungal clades, including but not limited to Neofabraea species causing tree cankers and bull's eye rot of apple (de Jong et al. 2001) and the Gibberella fujikuroi (Fusarium) species complex (O'Donnell et al. 1998b). ...
The internal transcribed spacer (ITS) DNA marker is routinely used for fungal identification but gives a clear result for only three out of four powdery mildew samples. A search for new markers indicates that some genes offer enhanced identification in comparison with ITS. Others fail due to amplification and sequencing difficulties and lack of informative variability. Powdery mildews (Ascomycota, Erysiphales) are biotrophic, fungal plant pathogens that commonly occur worldwide on a wide range of host plants. They are unsightly and greatly reduce the vigor of their hosts and have major impacts on crop and other cultivated plants. Species within this order are straightforward to spot, but difficult to identify. A citizen science scheme was run in 2013–2016 in the UK to gather a wide array of samples on which identification methods could be developed. Current techniques for identification and phylogenetic reconstruction show scope for improvement. In this paper, we review genes used in other fungal groups for discrimination at species level. Working protocols for amplification and sequencing of seven genes (actin, β-tubulin, calmodulin,Chs, elongation factor 1-α [EF1-α], Mcm7, and Tsr1) are developed with varying success; Mcm7 proves to be the most useful at differentiation between closely related, phylogenetically young powdery mildew species for phylogenetic reconstruction when used separately and in tandem with ITS. We therefore propose this as the most appropriate candidate gene to be used commonly in powdery mildew diagnostics alongside the ITS; furthermore, this could be transferred to similarly troublesome fungal clades.
