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Alternaria redefined.

Woudenberg JH, Groenewald JZ, Binder M, Crous PW - Stud. Mycol. (2013)

Bottom Line: Ulocladium Woudenb. & Crous, sect.Undifilum Woudenb. & Crous.New genus - Paradendryphiella Woudenb. & Crous.

View Article: PubMed Central - PubMed

Affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

ABSTRACT

Unlabelled: Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections.

Taxonomic novelties: New combinations - Alternaria abundans (E.G. Simmons) Woudenb. & Crous, Alternaria alternariae (Cooke) Woudenb. & Crous, Alternaria atra (Preuss) Woudenb. & Crous, Alternaria bornmuelleri (Magnus) Woudenb. & Crous, Alternaria botrytis (Preuss) Woudenb. & Crous, Alternaria caespitosa (de Hoog & C. Rubio) Woudenb. & Crous, Alternaria cantlous (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria caricis (E.G. Simmons) Woudenb. & Crous, Alternaria cinerea (Baucom & Creamer) Woudenb. & Crous, Alternaria didymospora (Munt.-Cvetk.) Woudenb. & Crous, Alternaria fulva (Baucom & Creamer) Woudenb. & Crous, Alternaria hyacinthi (de Hoog & P.J. Mull. bis) Woudenb. & Crous, Alternaria indefessa (E.G. Simmons) Woudenberg & Crous, Alternaria leptinellae (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria lolii (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria multiformis (E.G. Simmons) Woudenb. & Crous, Alternaria obclavata (Crous & U. Braun) Woudenb. & Crous, Alternaria obovoidea (E.G. Simmons) Woudenb. & Crous, Alternaria oudemansii (E.G. Simmons) Woudenb. & Crous, Alternaria oxytropis (Q. Wang, Nagao & Kakish.) Woudenb. & Crous, Alternaria penicillata (Corda) Woudenb. & Crous, Alternaria planifunda (E.G. Simmons) Woudenb. & Crous, Alternaria proteae (E.G. Simmons) Woudenb. & Crous, Alternaria scirpinfestans (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria scirpivora (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria septospora (Preuss) Woudenb. & Crous, Alternaria slovaca (Svob.-Pol., L. Chmel & Bojan.) Woudenb. & Crous, Alternaria subcucurbitae (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria tellustris (E.G. Simmons) Woudenb. & Crous, Alternaria tumida (E.G. Simmons) Woudenb. & Crous, Paradendryphiella salina (G.K. Sutherl.) Woudenb. & Crous, Paradendryphiella arenariae (Nicot) Woudenb. & Crous. New names - Alternaria aspera Woudenb. & Crous, Alternaria botryospora Woudenb. & Crous, Alternaria brassicae-pekinensis Woudenb. & Crous, Alternaria breviramosa Woudenb. & Crous, Alternaria chlamydosporigena Woudenb. & Crous, Alternaria concatenata Woudenb. & Crous, Alternaria embellisia Woudenb. & Crous, Alternaria heterospora Woudenb. & Crous, Alternaria papavericola Woudenb. & Crous, Alternaria terricola Woudenb. & Crous. Resurrected names - Alternaria cetera E.G. Simmons, Alternaria chartarum Preuss, Alternaria consortialis (Thüm.) J.W. Groves & S. Hughes, Alternaria cucurbitae Letendre & Roum., Alternaria dennisii M.B. Ellis, Alternaria eureka E.G. Simmons, Alternaria gomphrenae Togashi, Alternaria malorum (Ruehle) U. Braun, Crous & Dugan, Alternaria phragmospora Emden, Alternaria scirpicola (Fuckel) Sivan. New sections, all in Alternaria - sect. Chalastospora Woudenb. & Crous, sect. Cheiranthus Woudenb. & Crous, sect. Crivellia Woudenb. & Crous, sect. Dianthicola Woudenb. & Crous, sect. Embellisia Woudenb. & Crous, sect. Embellisioides Woudenb. & Crous, sect. Eureka Woudenb. & Crous, sect. Infectoriae Woudenb. & Crous, sect. Japonicae Woudenb. & Crous, sect. Nimbya Woudenb. & Crous, sect. Phragmosporae Woudenb. & Crous, sect. Pseudoulocladium Woudenb. & Crous, sect. Teretispora Woudenb. & Crous, sect. Ulocladioides Woudenb. & Crous, sect. Ulocladium Woudenb. & Crous, sect. Undifilum Woudenb. & Crous. New genus - Paradendryphiella Woudenb. & Crous.

No MeSH data available.


Related in: MedlinePlus

Bayesian 50 % majority rule consensus tree based on the GAPDH, RPB2 and TEF1 sequences of 121 strains representing the Alternaria complex. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to Stemphylium herbarum (CBS 191.86). The monotypic lineages are indicated by black dots.
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Figure 1: Bayesian 50 % majority rule consensus tree based on the GAPDH, RPB2 and TEF1 sequences of 121 strains representing the Alternaria complex. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to Stemphylium herbarum (CBS 191.86). The monotypic lineages are indicated by black dots.

Mentions: For defining the taxonomy of Alternaria and allied genera, 121 strains were included in the Alternaria complex alignment. The alignment length and unique site patterns of the different genes and gene combinations are stated in Table 2. The original ITS alignment consisted of 577 characters of which the first 78 are excluded as this contained a non-alignable region. In the original TEF1 alignment (375 characters) we coded the major inserts (Table 3), which otherwise would negatively influence the phylogeny, resulting in a TEF1 alignment of 269 characters. All phylogenies, different phylogenetic methods and gene regions or gene combinations used on this dataset (data not shown, trees and alignments lodged in TreeBASE), show a weak support at the deeper nodes of the tree. The only well-supported node (Bayesian posterior probability of 1.0, RAxML Maximum Likelihood support value of 100) in all phylogenies separates Embellisia annulataCBS 302.84 and the Pleospora/Stemphylium clade from the Alternaria complex (Fig. 1). In the Alternaria clade, six monotypic lineages and 24 internal clades occur consistently in the individual and combined phylogenies, although positions vary between the different gene regions or combinations used. The support values for the clades within Alternaria (called sections) are plotted in a heat map (Table 2) per gene and phylogenetic method used. The support values for the different phylogenetic methods vary, with the Bayesian posterior probabilities being higher than the RAxML bootstrap support values (Table 2). The SSU, LSU and ITS phylogenies display a low resolution, which reflects in poor to no support of the sections. Therefore, we chose not to include them in the multi-gene alignments, except in the all-gene alignment. In the GAPDH phylogenies, sect. Cheiranthus, sect. Nimbya and sect. Pseudoulocladium are poorly supported and “A. resedae” clusters separate from sect. Cheiranthus. In the RPB2 phylogenies the support values for sect. Alternata, sect. Embellisioides and sect. Eureka are relatively low; A. cumini clusters in sect. Embellisioides instead of sect. Eureka and U. capsici clusters separate from sect. Pseudoulocladium. The TEF1 phylogenies did not support sect. Nimbya and show relative low support for sect. Cheiranthus, sect. Dianthicola, sect. Embellisioides, sect. Panax, sect. Phragmosporae and sect. Radicina, and A. cumini clusters outside sect. Eureka. In the 2-region phylogenies U. capsici clusters outside sect. Pseudoulocladium based on GAPDH and RPB2, E. indefessa clusters outside sect. Cheiranthus based on GAPDH and TEF1, and sect. Eureka is poorly supported based on RPB2 and TEF1. The combined phylogeny based on the GAPDH, RPB2 and TEF1 sequences (Fig. 1) is displayed, as these are the genes with the best resolution.


Alternaria redefined.

Woudenberg JH, Groenewald JZ, Binder M, Crous PW - Stud. Mycol. (2013)

Bayesian 50 % majority rule consensus tree based on the GAPDH, RPB2 and TEF1 sequences of 121 strains representing the Alternaria complex. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to Stemphylium herbarum (CBS 191.86). The monotypic lineages are indicated by black dots.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3713888&req=5

Figure 1: Bayesian 50 % majority rule consensus tree based on the GAPDH, RPB2 and TEF1 sequences of 121 strains representing the Alternaria complex. The Bayesian posterior probabilities (PP) and RAxML bootstrap support values (ML) are given at the nodes (PP/ML). Thickened lines indicate a PP of 1.0 and ML of 100. The tree was rooted to Stemphylium herbarum (CBS 191.86). The monotypic lineages are indicated by black dots.
Mentions: For defining the taxonomy of Alternaria and allied genera, 121 strains were included in the Alternaria complex alignment. The alignment length and unique site patterns of the different genes and gene combinations are stated in Table 2. The original ITS alignment consisted of 577 characters of which the first 78 are excluded as this contained a non-alignable region. In the original TEF1 alignment (375 characters) we coded the major inserts (Table 3), which otherwise would negatively influence the phylogeny, resulting in a TEF1 alignment of 269 characters. All phylogenies, different phylogenetic methods and gene regions or gene combinations used on this dataset (data not shown, trees and alignments lodged in TreeBASE), show a weak support at the deeper nodes of the tree. The only well-supported node (Bayesian posterior probability of 1.0, RAxML Maximum Likelihood support value of 100) in all phylogenies separates Embellisia annulataCBS 302.84 and the Pleospora/Stemphylium clade from the Alternaria complex (Fig. 1). In the Alternaria clade, six monotypic lineages and 24 internal clades occur consistently in the individual and combined phylogenies, although positions vary between the different gene regions or combinations used. The support values for the clades within Alternaria (called sections) are plotted in a heat map (Table 2) per gene and phylogenetic method used. The support values for the different phylogenetic methods vary, with the Bayesian posterior probabilities being higher than the RAxML bootstrap support values (Table 2). The SSU, LSU and ITS phylogenies display a low resolution, which reflects in poor to no support of the sections. Therefore, we chose not to include them in the multi-gene alignments, except in the all-gene alignment. In the GAPDH phylogenies, sect. Cheiranthus, sect. Nimbya and sect. Pseudoulocladium are poorly supported and “A. resedae” clusters separate from sect. Cheiranthus. In the RPB2 phylogenies the support values for sect. Alternata, sect. Embellisioides and sect. Eureka are relatively low; A. cumini clusters in sect. Embellisioides instead of sect. Eureka and U. capsici clusters separate from sect. Pseudoulocladium. The TEF1 phylogenies did not support sect. Nimbya and show relative low support for sect. Cheiranthus, sect. Dianthicola, sect. Embellisioides, sect. Panax, sect. Phragmosporae and sect. Radicina, and A. cumini clusters outside sect. Eureka. In the 2-region phylogenies U. capsici clusters outside sect. Pseudoulocladium based on GAPDH and RPB2, E. indefessa clusters outside sect. Cheiranthus based on GAPDH and TEF1, and sect. Eureka is poorly supported based on RPB2 and TEF1. The combined phylogeny based on the GAPDH, RPB2 and TEF1 sequences (Fig. 1) is displayed, as these are the genes with the best resolution.

Bottom Line: Ulocladium Woudenb. & Crous, sect.Undifilum Woudenb. & Crous.New genus - Paradendryphiella Woudenb. & Crous.

View Article: PubMed Central - PubMed

Affiliation: CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

ABSTRACT

Unlabelled: Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections.

Taxonomic novelties: New combinations - Alternaria abundans (E.G. Simmons) Woudenb. & Crous, Alternaria alternariae (Cooke) Woudenb. & Crous, Alternaria atra (Preuss) Woudenb. & Crous, Alternaria bornmuelleri (Magnus) Woudenb. & Crous, Alternaria botrytis (Preuss) Woudenb. & Crous, Alternaria caespitosa (de Hoog & C. Rubio) Woudenb. & Crous, Alternaria cantlous (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria caricis (E.G. Simmons) Woudenb. & Crous, Alternaria cinerea (Baucom & Creamer) Woudenb. & Crous, Alternaria didymospora (Munt.-Cvetk.) Woudenb. & Crous, Alternaria fulva (Baucom & Creamer) Woudenb. & Crous, Alternaria hyacinthi (de Hoog & P.J. Mull. bis) Woudenb. & Crous, Alternaria indefessa (E.G. Simmons) Woudenberg & Crous, Alternaria leptinellae (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria lolii (E.G. Simmons & C.F. Hill) Woudenb. & Crous, Alternaria multiformis (E.G. Simmons) Woudenb. & Crous, Alternaria obclavata (Crous & U. Braun) Woudenb. & Crous, Alternaria obovoidea (E.G. Simmons) Woudenb. & Crous, Alternaria oudemansii (E.G. Simmons) Woudenb. & Crous, Alternaria oxytropis (Q. Wang, Nagao & Kakish.) Woudenb. & Crous, Alternaria penicillata (Corda) Woudenb. & Crous, Alternaria planifunda (E.G. Simmons) Woudenb. & Crous, Alternaria proteae (E.G. Simmons) Woudenb. & Crous, Alternaria scirpinfestans (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria scirpivora (E.G. Simmons & D.A. Johnson) Woudenb. & Crous, Alternaria septospora (Preuss) Woudenb. & Crous, Alternaria slovaca (Svob.-Pol., L. Chmel & Bojan.) Woudenb. & Crous, Alternaria subcucurbitae (Yong Wang bis & X.G. Zhang) Woudenb. & Crous, Alternaria tellustris (E.G. Simmons) Woudenb. & Crous, Alternaria tumida (E.G. Simmons) Woudenb. & Crous, Paradendryphiella salina (G.K. Sutherl.) Woudenb. & Crous, Paradendryphiella arenariae (Nicot) Woudenb. & Crous. New names - Alternaria aspera Woudenb. & Crous, Alternaria botryospora Woudenb. & Crous, Alternaria brassicae-pekinensis Woudenb. & Crous, Alternaria breviramosa Woudenb. & Crous, Alternaria chlamydosporigena Woudenb. & Crous, Alternaria concatenata Woudenb. & Crous, Alternaria embellisia Woudenb. & Crous, Alternaria heterospora Woudenb. & Crous, Alternaria papavericola Woudenb. & Crous, Alternaria terricola Woudenb. & Crous. Resurrected names - Alternaria cetera E.G. Simmons, Alternaria chartarum Preuss, Alternaria consortialis (Thüm.) J.W. Groves & S. Hughes, Alternaria cucurbitae Letendre & Roum., Alternaria dennisii M.B. Ellis, Alternaria eureka E.G. Simmons, Alternaria gomphrenae Togashi, Alternaria malorum (Ruehle) U. Braun, Crous & Dugan, Alternaria phragmospora Emden, Alternaria scirpicola (Fuckel) Sivan. New sections, all in Alternaria - sect. Chalastospora Woudenb. & Crous, sect. Cheiranthus Woudenb. & Crous, sect. Crivellia Woudenb. & Crous, sect. Dianthicola Woudenb. & Crous, sect. Embellisia Woudenb. & Crous, sect. Embellisioides Woudenb. & Crous, sect. Eureka Woudenb. & Crous, sect. Infectoriae Woudenb. & Crous, sect. Japonicae Woudenb. & Crous, sect. Nimbya Woudenb. & Crous, sect. Phragmosporae Woudenb. & Crous, sect. Pseudoulocladium Woudenb. & Crous, sect. Teretispora Woudenb. & Crous, sect. Ulocladioides Woudenb. & Crous, sect. Ulocladium Woudenb. & Crous, sect. Undifilum Woudenb. & Crous. New genus - Paradendryphiella Woudenb. & Crous.

No MeSH data available.


Related in: MedlinePlus