{"id":2251,"date":"2022-09-22T17:19:14","date_gmt":"2022-09-22T17:19:14","guid":{"rendered":"https:\/\/magnaporthales.sebs.rutgers.edu\/?p=2251"},"modified":"2022-10-04T00:48:35","modified_gmt":"2022-10-04T00:48:35","slug":"taxonomy-and-phylogeny","status":"publish","type":"post","link":"https:\/\/magnaporthales.sebs.rutgers.edu\/?p=2251","title":{"rendered":"Taxonomy and phylogeny"},"content":{"rendered":"\n<p><img loading=\"lazy\" class=\"aligncenter wp-image-2277\" src=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig1.1.2.3.all_.16200.jpg\" alt=\"\" width=\"1000\" height=\"387\" srcset=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig1.1.2.3.all_.16200.jpg 1260w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig1.1.2.3.all_.16200-300x116.jpg 300w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig1.1.2.3.all_.16200-1024x396.jpg 1024w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig1.1.2.3.all_.16200-768x297.jpg 768w\" sizes=\"(max-width: 1000px) 100vw, 1000px\" \/><br \/>Fig. 1.1. Sclerotia of the rice stem rot fungus <em>Nakataea oryzae<\/em>, scale bar = 200 \u00b5m. 1.2. Perithecium (left, scale bar = 100 \u00b5m), ascus and ascospores (right, scale bar = 10 \u00b5m) of <em>Magnaporthiopsis poae<\/em>. 1.3.\u00a0 Pear-shaped conidia of <em>Pyricularia grisea<\/em>,\u00a0scale bar = 10 \u00b5m.<br \/>\u00a0<br \/>\u00a0 \u00a0 The first described species in <em>Magnaporthales<\/em> was the rice stem rot fungus. The stem rot fungus, as <em>Sclerotium oryzae<\/em>, based on the sclerotial morph was named in 1877 (Cattaneo, 1877) (Fig. 1.1). Its conidial morphs were subsequently named <em>Nakataea sigmoidea<\/em> in 1939 (Hara, 1939). The sexual morph of this fungus was not discovered until after almost a century later. Krause and Webster (1972) established a new genus <em>Magnaporthe<\/em> in <em>Diaporthales<\/em> to accommodate the sexual morph of this species as <em>Magnaporthe salvinii<\/em> (Krause and Webster, 1972). Four more species have been placed in <em>Magnaporthe<\/em> based on their sexual morphology: <em>M. grisea<\/em>, <em>M. oryzae<\/em>, <em>M. poae<\/em>, and <em>M. rhizophila<\/em>. (Fig. 1.2).<br \/>\u00a0 \u00a0 In 1880, Saccardo established the genus <em>Pyricularia<\/em> (pyri: pear-shaped conidia, Fig. 1.3) based on <em>P. grisea<\/em> on crabgrass (Saccardo, 1880) including primarily asexual species. The rice isolates were designated as <em>P. oryzae<\/em> by Cavara (1892), which now is known as the rice blast fungus. Since then, over 70 names have been placed in <em>Pyricularia<\/em> many of which cause blast diseases of monocotyledonous plants. However, only a fraction of <em>Pyricularia<\/em> species have been included in modern phylogenetic analyses (Tosa and Chuma, 2014). <br \/>\u00a0 \u00a0 The sexual morph of <em>P. grisea<\/em> was first developed from crossing experiments in culture by Hebert (Hebert, 1971) and it was placed in <em>Ceratosphaeria<\/em>. Barr (1977) later moved it to <em>Magnaporthe<\/em> because of the similarity in ascospore morphology to the type species <em>M. salvini<\/em>i. The sexual morph of the rice blast fungus also was obtained by laboratory crossing experiments and was named <em>M. oryzae<\/em> (Couch and Kohn, 2002). Recent phylogenetic and phylogenomic analyses demonstrate that the rice blast fungus does not belong to <em>Magnaporthe<\/em> (Luo et al., 2015a; Luo and Zhang, 2013; Murata et al., 2014; Zhang et al., 2011) (Fig. 1.4). Rather the type of <em>Magnaporthe<\/em>, <em>M. salvinii<\/em>, belongs in <em>Magnaporthaceae<\/em> and is not congeneric with <em>P. grisea<\/em> and <em>P. oryzae<\/em> placed in <em>Pyriculariaceae<\/em>. Placement of the sexual morph of the rice blast fungus, <em>P. oryzae<\/em>, in <em>Magnaporthe<\/em> was based on incomplete data.<br \/>\u00a0 \u00a0 Traditionally, mycologists have given considerable weight to ascospore morphology, such as shape, size, pigmentation, and wall ornamentation, in delimiting genera in ascomycetes. With the development of polymerase chain reaction (PCR) and DNA sequencing technology in the early 1990s, molecular phylogeny has become a powerful approach for understanding fungal systematics. Molecular phylogenetic studies suggest that taxonomy based on traditional morphological characteristics does not always reflect evolutionary history. A 6-gene phylogeny, specifically the largest subunit of RNA polymerase II gene (<em>RPB1<\/em>), translation elongation factor 1-alpha gene (<em>TEF1<\/em>), a DNA replication licensing factor gene (<em>MCM7<\/em>), the internal transcribed spacer region of the nuclear rRNA genes (ITS), 18S rRNA gene (18S), and 28S rRNA gene (28S), has been applied to genera in <em>Magnaporthales<\/em>. Zhang et al. (2011) pointed out that both <em>Gaeumannomyces<\/em> and <em>Magnaporthe<\/em>, two important genera in <em>Magnaporthales<\/em>, are polyphyletic. Taxonomic revisions of these taxa subsequently have been made by Luo and Zhang (2013), Klaubauf et al. (2014), Hern\u00e1ndez-Restrepo et al. (2016) and Zhang et al. (2016). Pathology and characteristics of the asexual morph, rather than ascospore morphology, correspond better with phylogenetic relationships of these fungi. The 6-gene phylogeny also recognizes two major clades in these fungi, one clade includes root-infecting species that produce phialophora-like conidia, while the other clade includes fungi causing blast diseases that produce pyricularia-like conidia (Zhang et al., 2011).<br \/>\u00a0 \u00a0 The family <em>Magnaporthaceae<\/em> was proposed for a group of cereal and grass-associated fungi centered on species causing rice stem rot and blast symptoms, along with <em>Buergenerula<\/em>, <em>Clasterosphaeria<\/em>, <em>Gaeumannomyces<\/em>, <em>Herbampulla<\/em>, and <em>Omnidemptus<\/em>, most of which are necrotrophic or hemibiotrophic pathogens (Cannon 1994). Early taxonomic studies had placed the rice blast fungus and allied species in different orders in Ascomycota, such as <em>Diaporthales<\/em>, <em>Phyllachorales<\/em>, and <em>Xylariales<\/em> (Barr, 1977; Krause and Webster, 1972). Later molecular phylogenetic analyses supported a monophyletic <em>Magnaporthaceae<\/em> as defined by (Cannon, 1994) placing it in subclass <em>Sordariomycetidae<\/em> (<em>Sordariomycetes<\/em>, <em>Ascomycota<\/em>). However, subsequent analyses supported variable phylogenetic affinities for this family. For example, in Zhang and Blackwell\u2019s (2001) 18S rDNA tree, <em>Magnaporthaceae<\/em> formed a sister clade with <em>Ophiostomatales<\/em>. The 28S rDNA tree generated by Huhndorf et al. (2008) proposed a close relationship of <em>Magnaporthaceae<\/em> with <em>Sordariales<\/em>, Chaetosphaeriales and Boliniales (Huhndorf et al., 2008). In the 18S tree of Thongkantha et al. (2009), the <em>Magnaporthaceae<\/em> formed a clade sister to <em>Diaporthales<\/em> and <em>Ophiostomatales<\/em>; however, in the same paper, the 28S rDNA tree grouped them with <em>Chaetosphaeriales<\/em> and <em>Sordariaceae<\/em> (Thongkantha et al., 2009). Zhang et al. (2006) generated a four-gene phylogeny (<em>TEF1<\/em>; the second largest subunit of RNA polymerase II, <em>RPB2<\/em>; 18S and 28S) and suggested that the rice blast fungus was most closely related to <em>Diaporthales<\/em>. However, no other taxa in <em>Magnaporthaceae<\/em> were included in the analysis (Zhang et al., 2006). Poor taxon sampling due to a lack of sequence data from non-model species in <em>Magnaporthaceae<\/em> and phylogenetic heterogeneity among gene loci (Ebersberger et al., 2012; Fitzpatrick et al., 2006) likely explain the conflicting tree topologies in these studies. <br \/>\u00a0 \u00a0 In 2009, a new order, <em>Magnaporthales<\/em>, with a single family was established (Thongkantha et al., 2009), characterized by nonstromatic black perithecia, usually with long hairy necks, persistent asci, and fusiform (spindle-shaped) or filiform (needle-shaped) ascospores. The asexual morphs are hyphomycetous and variable but can be categorized as two types: pyricularia-like or phialophora-like (Fig. 1.4). Several asexual genera have been linked to <em>Magnaporthales<\/em>, including <em>Clasterosporium<\/em>, <em>Didymobotryum<\/em>, <em>Harpophora<\/em>, <em>Mycoleptodiscus<\/em>, <em>Nakataea<\/em>, <em>Phialophora<\/em>, <em>Pseudotracylla<\/em>, <em>Pyricularia<\/em>, <em>Sclerotium<\/em>, and <em>Trichocladium<\/em> (Cannon, 1994; Cannon and Alcorn, 1994; Gams, 2000; Huhndorf et al., 2008; Kohlmeyer and Volkmann-Kohlmeyer, 1995; Thongkantha et al., 2009). Currently <em>Clasterosporium<\/em>, <em>Nakataea<\/em>, <em>Pseudotracylla<\/em>, and <em>Pyricularia<\/em> are maintained in <em>Magnaporthales<\/em> (Luo and Zhang, 2013; Zhang et al., 2016). <em>Harpophora<\/em> is treated as a synonym of <em>Gaeumannomyces<\/em> (Luo et al., 2015b) while <em>Didymobotryum<\/em>, <em>Mycoleptodiscus<\/em>, Phialophora, <em>Sclerotium<\/em> and <em>Trichocladium<\/em> are excluded from <em>Magnaporthales<\/em> (Klaubauf et al., 2014). Some pathogenic species produce specialized infection structures when colonizing their host plants, known as appressoria and hyphopodia. The hyphal pressing organs can generate strong turgor pressure to penetrate the host cells (Dean et al., 2005). <em>Magnaporthales<\/em> currently contains over 200 species. In addition, an increasing number of environmental sequences of uncultured <em>Magnaporthales<\/em> have been deposited in GenBank, suggesting cryptic diversity of <em>Magnaporthales<\/em>.<br \/>\u00a0 \u00a0 To generate a robust phylogeny for <em>Magnaporthales<\/em>, Luo et al. (2015a) performed a phylogenomic analysis using more than 200 genes, which supported <em>Magnaporthales<\/em> as a monophyletic order, sister to <em>Ophiostomatales<\/em> (Fig. 1.5) (Luo et al., 2015a). This result is consistent with the shared characteristics between the two orders: both have non-stromatic perithecia and a hyphomycetous asexual morph. In contrast, species in <em>Diaporthales<\/em> typically produce stromatic perithecia and a coelomycetous asexual morph. Within <em>Magnaporthales<\/em>, the phylogenomic analysis resulted in three well-supported clades: 1) an early diverging clade A comprised of saprotrophs associated with submerged wood; 2) clade B that includes the rice blast fungus and other pathogens that cause blast diseases of monocot plants. These species infect the above-ground tissues of host plants using a penetration structure, the appressorium; and 3) clade C comprised primarily of root-associated species that penetrate the root tissue with hyphopodia (Fig. 1.4). These three clades correspond to the families <em>Magnaporthaceae<\/em>, <em>Ophioceraceae<\/em>, and <em>Pyriculariaceae<\/em> as classified by Klaubauf et al. (2014) based on a 2-locus (28S and RPB1) phylogeny (Klaubauf et al., 2014). The early diverging lineage of <em>Magnaporthales<\/em>, namely <em>Ophioceraceae<\/em> (clade A) is mostly aquatic and saprotrophic on wood substrates. The pathogenicity of the remaining lineages is likely a derived feature from <em>Pyriculariaceae<\/em> (clade B), which evolved to infect host aerial parts using appressoria, and <em>Magnaporthaceae<\/em> (clade C) adapted to plant root infection with hyphopodia (Luo et al., 2015a). These well-supported phylogenies provide a robust framework for elucidating evolution of pathogenesis, nutrition modes, and phenotypic characters in <em>Magnaporthales<\/em>.<br \/><img loading=\"lazy\" class=\"aligncenter wp-image-2259\" src=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.4_200711.120.jpg\" alt=\"\" width=\"1000\" height=\"750\" srcset=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.4_200711.120.jpg 756w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.4_200711.120-300x225.jpg 300w\" sizes=\"(max-width: 1000px) 100vw, 1000px\" \/><br \/>Fig. 1.4. Maximum likelihood tree of 24 <em>Magnaporthales<\/em> species and five <em>Sordariomycetes<\/em> used as outgroup species based on 82,715 amino acid positions derived from 226 genes. The infection sites and the morphology of sexual and asexual states for the three major <em>Magnaporthales<\/em> clades are illustrated (right panel). The supporting values for each node were estimated using 1000 bootstrap replicates. The strain number and genome size (if available) for each species are provided (Luo et al. 2015a).<br \/>*<em>Buergenerula spartinae<\/em>, <em>Bussabanomyces longisporus<\/em>, <em>Nakataea oryzae<\/em>, and <em>Omnidemptus affinis<\/em> are associated with above-ground parts of host plants, which is an exception in clade C. <em>Pyricularia oryzae<\/em> is associated with both the leaf and root of the host plant, which is an exception in clade B.<br \/><img loading=\"lazy\" class=\"aligncenter wp-image-2260\" src=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.5_200711.120.jpg\" alt=\"\" width=\"1000\" height=\"750\" srcset=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.5_200711.120.jpg 756w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.5_200711.120-300x225.jpg 300w\" sizes=\"(max-width: 1000px) 100vw, 1000px\" \/><br \/>Fig. 1.5. Maximum likelihood tree of 21 <em>Pezizomycotina<\/em> species and two <em>Saccharomycetes<\/em> used as outgroup species based on 83,616 amino acid positions derived from 226 genes. The morphology of the sexual and asexual states for <em>Magnaporthales<\/em> and closely related species is shown (right panel). The supporting values for each node were estimated using 1000 bootstrap replicates. The strain number and genome size for each species are provided (Luo et al. 2015a).<br \/><br \/>\u00a0 \u00a0 In this monograph, we analyzed a number of DNA sequence data for several understudied taxa of <em>Magnaporthales<\/em>, such as <em>Ceratosphaerella<\/em>, <em>Muraeriata,<\/em> and <em>Tropohalonectria<\/em> in order to resolve their phylogenetic positions.<br \/><img loading=\"lazy\" class=\"aligncenter wp-image-2261\" src=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.6_200711.120.jpg\" alt=\"\" width=\"1000\" height=\"1294\" srcset=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.6_200711.120.jpg 756w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.6_200711.120-232x300.jpg 232w\" sizes=\"(max-width: 1000px) 100vw, 1000px\" \/><br \/>Fig. 1.6. Maximum likelihood trees inferred from the combined ITS, 28S, and TEF1 gene sequences without constraint (A), and with <em>Magnaporthaceae<\/em>, <em>Pyriculariaceae<\/em>, and <em>Ophioceraceae<\/em> as constraints (B). ML bootstrap values and BI posterior probabilities are indicated above internodes.<br \/><img loading=\"lazy\" class=\"aligncenter wp-image-2262\" src=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.7_200711.120.jpg\" alt=\"\" width=\"1000\" height=\"1294\" srcset=\"https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.7_200711.120.jpg 756w, https:\/\/magnaporthales.sebs.rutgers.edu\/wp-content\/uploads\/2022\/09\/Fig.1.7_200711.120-232x300.jpg 232w\" sizes=\"(max-width: 1000px) 100vw, 1000px\" \/>Fig. 1.7. Maximum likelihood trees inferred from the 28S gene sequences without constraint (A), and with <em>Magnaporthaceae<\/em>, <em>Pyriculariaceae<\/em>, and <em>Ophioceraceae<\/em> as constraints (B). ML bootstrap values and BI posterior probabilities are indicated above internodes.<br \/><br \/>\u00a0 \u00a0 Previously <em>Ceratosphaerella<\/em> and <em>Muraeriata<\/em> had been placed in <em>Magnaporthaceae<\/em> and shared similarities with <em>Ceratosphaeria<\/em>, <em>Ophioceras<\/em>, and <em>Pseudohalonectria<\/em>, including long-necked perithecia, woody habitats and saprobic habit (Huhndorf et al., 2008). However, our results suggested a close relationship between Ophioceras and Ceratosphaerella within the family Ophioceraceae. <em>Muraeriata<\/em> fell into the family <em>Magnaporthaceae<\/em>, showing affinity with <em>Aquafiliformis<\/em>. Unlike other plant pathogenic family members, both genera are saprobic.<br \/>\u00a0 \u00a0 <em>Tropohalonectria<\/em> was proposed for a species that was previously treated as <em>Pseudohalonectria<\/em> but genetically different from <em>Pseudohalonectria sensu stricto<\/em>. It was phylogenetically basal in <em>Magnaporthales<\/em> (Perera et al., 2016). Our study showed similar results and supported its placement in <em>Ophioceraceae<\/em>.<br \/>\u00a0 \u00a0 Phylogenies generated in this study corroborate the three-family system of <em>Magnaporthales<\/em> according to Klaubauf et al. (2014) and Luo et al. (2015a). Recently the family <em>Ophioceraceae<\/em> was further split into three families by Hongsanan et al (Hongsanan et al., 2017) and Luo et al. (Luo et al., 2019). However, the two new families <em>Pseudohalonectriaceae<\/em> and <em>Ceratosphaeriaceae<\/em> were both based on a single genus and lacked adequate morphological or biological differences to differentiate them at the family level. Therefore, we follow the family circumscription of <em>Ophioceraceae sensu<\/em> Klaubauf et al. (Klaubauf et al., 2014). In this monograph, the three-family system is adopted, and the placement of genera at the family level is inferred from the ITS, 28S, and TEF1 gene (Fig. 1.6) and the 28S gene only phylogenies (Fig. 1.7).<br \/><br \/><span style=\"font-family: arial, helvetica, sans-serif;\">Copyright 2022 by The American Phytopathological Society. Reproduced, by permission, from Luo, J., and Zhang, N. 2022. <a href=\"https:\/\/my.apsnet.org\/APSStore\/APSStore\/Product-Detail.aspx?iProductCode=46826.\">The Rice Blast Fungus and Allied Species: A Monograph of the Fungal Order <em>Magnaporthales<\/em><\/a>\u00a0(<a href=\"https:\/\/my.apsnet.org\/APSStore\/Product-Detail.aspx?WebsiteKey=2661527A-8D44-496C-A730-8CFEB6239BE7&amp;iProductCode=46826\">https:\/\/my.apsnet.org\/APSStore\/Product-Detail.aspx?WebsiteKey=2661527A-8D44-496C-A730-8CFEB6239BE7&amp;iProductCode=46826<\/a>).\u00a0American Phytopathological Society, St. Paul, MN.\u00a0<\/span><br \/><br \/><\/p>\n<p>\u00a0<\/p>\n<p>\u00a0<\/p>\n<p>\u00a0<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Fig. 1.1. Sclerotia of the rice stem rot fungus Nakataea oryzae, scale bar = 200 \u00b5m. 1.2. Perithecium (left, scale bar = 100 \u00b5m), ascus and ascospores (right, scale bar = 10 \u00b5m) of Magnaporthiopsis poae. 1.3.\u00a0 Pear-shaped conidia of Pyricularia grisea,\u00a0scale bar = 10 \u00b5m.\u00a0\u00a0 \u00a0 The first described species in Magnaporthales was the &#8230; <a title=\"Taxonomy and phylogeny\" class=\"read-more\" href=\"https:\/\/magnaporthales.sebs.rutgers.edu\/?p=2251\" aria-label=\"More on Taxonomy and phylogeny\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[82],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v19.7.1 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\r\n<title>Taxonomy and phylogeny - An E-monograph of the Fungal Order Magnaporthales: Taxonomy, Molecular Phylogeny, and Biogeography<\/title>\r\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\r\n<link rel=\"canonical\" href=\"https:\/\/magnaporthales.sebs.rutgers.edu\/?p=2251\" \/>\r\n<meta property=\"og:locale\" content=\"en_US\" \/>\r\n<meta property=\"og:type\" content=\"article\" \/>\r\n<meta property=\"og:title\" content=\"Taxonomy and phylogeny - An E-monograph of the Fungal Order Magnaporthales: Taxonomy, Molecular Phylogeny, and Biogeography\" \/>\r\n<meta property=\"og:description\" content=\"Fig. 1.1. Sclerotia of the rice stem rot fungus Nakataea oryzae, scale bar = 200 \u00b5m. 1.2. Perithecium (left, scale bar = 100 \u00b5m), ascus and ascospores (right, scale bar = 10 \u00b5m) of Magnaporthiopsis poae. 1.3.\u00a0 Pear-shaped conidia of Pyricularia grisea,\u00a0scale bar = 10 \u00b5m.\u00a0\u00a0 \u00a0 The first described species in Magnaporthales was the ... 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Sclerotia of the rice stem rot fungus Nakataea oryzae, scale bar = 200 \u00b5m. 1.2. Perithecium (left, scale bar = 100 \u00b5m), ascus and ascospores (right, scale bar = 10 \u00b5m) of Magnaporthiopsis poae. 1.3.\u00a0 Pear-shaped conidia of Pyricularia grisea,\u00a0scale bar = 10 \u00b5m.\u00a0\u00a0 \u00a0 The first described species in Magnaporthales was the ... 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