A class-wide phylogenetic assessment of Dothideomycetes

C. L. Schoch; P. W. Crous; J. Z. Groenewald; E. W.A. Boehm; T. I. Burgess; J. de Gruyter; G. S. de Hoog; L. J. Dixon; M. Grube; C. Gueidan; Y. Harada; S. Hatakeyama; K. Hirayama; T. Hosoya; S. M. Huhndorf; K. D. Hyde; E. B.G. Jones; J. Kohlmeyer; Å Kruys; Y. M. Li; R. Lücking; H. T. Lumbsch; L. Marvanová; J. S. Mbatchou; A. H. McVay; A. N. Miller; G. K. Mugambi; L. Muggia; M. P. Nelsen; P. Nelson; C. A. Owensby; A. J.L. Phillips; S. Phongpaichit; S. B. Pointing; V. Pujade-Renaud; H. A. Raja; E. Rivas Plata; B. Robbertse; C. Ruibal; J. Sakayaroj; T. Sano; L. Selbmann; C. A. Shearer; T. Shirouzu; B. Slippers; S. Suetrong; K. Tanaka; B. Volkmann-Kohlmeyer; M. J. Wingfield; A. R. Wood; J. H.C. Woudenberg; H. Yonezawa; Y. Zhang; J. W. Spatafora

doi:10.3114/sim.2009.64.01

A class-wide phylogenetic assessment of Dothideomycetes

C. L. Schoch, P. W. Crous, J. Z. Groenewald, E. W.A. Boehm, T. I. Burgess, J. de Gruyter, G. S. de Hoog, L. J. Dixon, M. Grube, C. Gueidan, Y. Harada, S. Hatakeyama, K. Hirayama, T. Hosoya, S. M. Huhndorf, K. D. Hyde, E. B.G. Jones, J. Kohlmeyer, Å Kruys, Y. M. LiR. Lücking, H. T. Lumbsch, L. Marvanová, J. S. Mbatchou, A. H. McVay, A. N. Miller, G. K. Mugambi, L. Muggia, M. P. Nelsen, P. Nelson, C. A. Owensby, A. J.L. Phillips, S. Phongpaichit, S. B. Pointing, V. Pujade-Renaud, H. A. Raja, E. Rivas Plata, B. Robbertse, C. Ruibal, J. Sakayaroj, T. Sano, L. Selbmann, C. A. Shearer, T. Shirouzu, B. Slippers, S. Suetrong, K. Tanaka, B. Volkmann-Kohlmeyer, M. J. Wingfield, A. R. Wood, J. H.C. Woudenberg, H. Yonezawa, Y. Zhang, J. W. Spatafora

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Abstract

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Original language	English (US)
Pages (from-to)	1-15
Number of pages	15
Journal	Studies in Mycology
Volume	64
DOIs	https://doi.org/10.3114/sim.2009.64.01
State	Published - Dec 2009

Keywords

Ascomycota
Dothideomyceta
Fungal evolution
Lichens
Multigene phylogeny
Pezizomycotina
Phylogenomics
Plant pathogens
Saprobes
Tree of life

ASJC Scopus subject areas

Agricultural and Biological Sciences (miscellaneous)

Online availability

10.3114/sim.2009.64.01

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Schoch, C. L., Crous, P. W., Groenewald, J. Z., Boehm, E. W. A., Burgess, T. I., de Gruyter, J., de Hoog, G. S., Dixon, L. J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S. M., Hyde, K. D., Jones, E. B. G., Kohlmeyer, J., Kruys, Å., ... Spatafora, J. W. (2009). A class-wide phylogenetic assessment of Dothideomycetes. Studies in Mycology, 64, 1-15. https://doi.org/10.3114/sim.2009.64.01

Schoch, CL, Crous, PW, Groenewald, JZ, Boehm, EWA, Burgess, TI, de Gruyter, J, de Hoog, GS, Dixon, LJ, Grube, M, Gueidan, C, Harada, Y, Hatakeyama, S, Hirayama, K, Hosoya, T, Huhndorf, SM, Hyde, KD, Jones, EBG, Kohlmeyer, J, Kruys, Å, Li, YM, Lücking, R, Lumbsch, HT, Marvanová, L, Mbatchou, JS, McVay, AH, Miller, AN, Mugambi, GK, Muggia, L, Nelsen, MP, Nelson, P, Owensby, CA, Phillips, AJL, Phongpaichit, S, Pointing, SB, Pujade-Renaud, V, Raja, HA, Plata, ER, Robbertse, B, Ruibal, C, Sakayaroj, J, Sano, T, Selbmann, L, Shearer, CA, Shirouzu, T, Slippers, B, Suetrong, S, Tanaka, K, Volkmann-Kohlmeyer, B, Wingfield, MJ, Wood, AR, Woudenberg, JHC, Yonezawa, H, Zhang, Y & Spatafora, JW 2009, 'A class-wide phylogenetic assessment of Dothideomycetes', Studies in Mycology, vol. 64, pp. 1-15. https://doi.org/10.3114/sim.2009.64.01

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title = "A class-wide phylogenetic assessment of Dothideomycetes",

abstract = "We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.",

keywords = "Ascomycota, Dothideomyceta, Fungal evolution, Lichens, Multigene phylogeny, Pezizomycotina, Phylogenomics, Plant pathogens, Saprobes, Tree of life",

author = "Schoch, {C. L.} and Crous, {P. W.} and Groenewald, {J. Z.} and Boehm, {E. W.A.} and Burgess, {T. I.} and {de Gruyter}, J. and {de Hoog}, {G. S.} and Dixon, {L. J.} and M. Grube and C. Gueidan and Y. Harada and S. Hatakeyama and K. Hirayama and T. Hosoya and Huhndorf, {S. M.} and Hyde, {K. D.} and Jones, {E. B.G.} and J. Kohlmeyer and {\AA} Kruys and Li, {Y. M.} and R. L{\"u}cking and Lumbsch, {H. T.} and L. Marvanov{\'a} and Mbatchou, {J. S.} and McVay, {A. H.} and Miller, {A. N.} and Mugambi, {G. K.} and L. Muggia and Nelsen, {M. P.} and P. Nelson and Owensby, {C. A.} and Phillips, {A. J.L.} and S. Phongpaichit and Pointing, {S. B.} and V. Pujade-Renaud and Raja, {H. A.} and Plata, {E. Rivas} and B. Robbertse and C. Ruibal and J. Sakayaroj and T. Sano and L. Selbmann and Shearer, {C. A.} and T. Shirouzu and B. Slippers and S. Suetrong and K. Tanaka and B. Volkmann-Kohlmeyer and Wingfield, {M. J.} and Wood, {A. R.} and Woudenberg, {J. H.C.} and H. Yonezawa and Y. Zhang and Spatafora, {J. W.}",

note = "Funding Information: Authors from individual papers in this volume contributed to this work and specific acknowledgements to that regard can be found in individual papers. Work performed for this paper by the first author after 2008 was supported in part by the Intramural Research Program of the NIH, National Library of Medicine. Part of this work was also funded by grants from NSF (DEB-0717476) to J. W. Spatafora (and C.L. Schoch until 2008) and (DEB-0732993) to J.W. Spatafora and B. Robbertse.",

year = "2009",

month = dec,

doi = "10.3114/sim.2009.64.01",

language = "English (US)",

volume = "64",

pages = "1--15",

journal = "Studies in Mycology",

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T1 - A class-wide phylogenetic assessment of Dothideomycetes

AU - Schoch, C. L.

AU - Crous, P. W.

AU - Groenewald, J. Z.

AU - Boehm, E. W.A.

AU - Burgess, T. I.

AU - de Gruyter, J.

AU - de Hoog, G. S.

AU - Dixon, L. J.

AU - Grube, M.

AU - Gueidan, C.

AU - Harada, Y.

AU - Hatakeyama, S.

AU - Hirayama, K.

AU - Hosoya, T.

AU - Huhndorf, S. M.

AU - Hyde, K. D.

AU - Jones, E. B.G.

AU - Kohlmeyer, J.

AU - Kruys, Å

AU - Li, Y. M.

AU - Lücking, R.

AU - Lumbsch, H. T.

AU - Marvanová, L.

AU - Mbatchou, J. S.

AU - McVay, A. H.

AU - Miller, A. N.

AU - Mugambi, G. K.

AU - Muggia, L.

AU - Nelsen, M. P.

AU - Nelson, P.

AU - Owensby, C. A.

AU - Phillips, A. J.L.

AU - Phongpaichit, S.

AU - Pointing, S. B.

AU - Pujade-Renaud, V.

AU - Raja, H. A.

AU - Plata, E. Rivas

AU - Robbertse, B.

AU - Ruibal, C.

AU - Sakayaroj, J.

AU - Sano, T.

AU - Selbmann, L.

AU - Shearer, C. A.

AU - Shirouzu, T.

AU - Slippers, B.

AU - Suetrong, S.

AU - Tanaka, K.

AU - Volkmann-Kohlmeyer, B.

AU - Wingfield, M. J.

AU - Wood, A. R.

AU - Woudenberg, J. H.C.

AU - Yonezawa, H.

AU - Zhang, Y.

AU - Spatafora, J. W.

N1 - Funding Information: Authors from individual papers in this volume contributed to this work and specific acknowledgements to that regard can be found in individual papers. Work performed for this paper by the first author after 2008 was supported in part by the Intramural Research Program of the NIH, National Library of Medicine. Part of this work was also funded by grants from NSF (DEB-0717476) to J. W. Spatafora (and C.L. Schoch until 2008) and (DEB-0732993) to J.W. Spatafora and B. Robbertse.

PY - 2009/12

Y1 - 2009/12

N2 - We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

AB - We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

KW - Ascomycota

KW - Dothideomyceta

KW - Fungal evolution

KW - Lichens

KW - Multigene phylogeny

KW - Pezizomycotina

KW - Phylogenomics

KW - Plant pathogens

KW - Saprobes

KW - Tree of life

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UR - http://www.scopus.com/inward/citedby.url?scp=77954765891&partnerID=8YFLogxK

U2 - 10.3114/sim.2009.64.01

DO - 10.3114/sim.2009.64.01

M3 - Article

C2 - 20169021

AN - SCOPUS:77954765891

SN - 0166-0616

VL - 64

SP - 1

EP - 15

JO - Studies in Mycology

JF - Studies in Mycology

ER -

A class-wide phylogenetic assessment of Dothideomycetes

Abstract

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