Resolution of deep divergence of club fungi (phylum Basidiomycota)

doi:10.1016/j.synbio.2019.12.001

. 2019 Dec 10;4(4):225-231.

doi: 10.1016/j.synbio.2019.12.001. eCollection 2019 Dec.

Resolution of deep divergence of club fungi (phylum Basidiomycota)

Hongliang Mao¹, Hao Wang¹

Affiliations

PMID: 31890927
PMCID: PMC6926304
DOI: 10.1016/j.synbio.2019.12.001

Resolution of deep divergence of club fungi (phylum Basidiomycota)

Hongliang Mao et al. Synth Syst Biotechnol. 2019.

. 2019 Dec 10;4(4):225-231.

doi: 10.1016/j.synbio.2019.12.001. eCollection 2019 Dec.

Authors

Hongliang Mao¹, Hao Wang¹

Affiliation

¹ T-Life Research Center, Department of Physics, Fudan University, Shanghai, 200433, PR China.

PMID: 31890927
PMCID: PMC6926304
DOI: 10.1016/j.synbio.2019.12.001

Erratum in

Erratum regarding previously published articles.
[No authors listed] [No authors listed] Synth Syst Biotechnol. 2020 Dec;5(4):329. doi: 10.1016/j.synbio.2020.10.002. Epub 2020 Oct 14. Synth Syst Biotechnol. 2020. PMID: 33072899 Free PMC article.

Abstract

A long-standing question about the early evolution of club fungi (phylum Basidiomycota) is the relationship between the three major groups, Pucciniomycotina, Ustilaginomycotina and Agaricomycotina. It is unresolved whether Agaricomycotina are more closely related to Ustilaginomycotina or to Pucciniomycotina. Here we reconstructed the branching order of the three subphyla through two sources of phylogenetic signals, i.e. standard phylogenomic analysis and alignment-free phylogenetic approach. Overall, beyond congruency within the frame of standard phylogenomic analysis, our results consistently and robustly supported the early divergence of Ustilaginomycotina and a closer relationship between Agaricomycotina and Pucciniomycotina.

Keywords: Basidiomycota; CVTree; Fungi; Phylogenetics; Phylogenomics.

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Figures

**Fig. 1**
The most likely evolutionary relationship involving the three subphyla of Basidiomycota. The tree shows higher-than-order level relationships of the majority rule consensus of 4 standard phylogenomic reconstructions of 91 genomes using 171 gene clusters. Statistical supports are numbers attached to nodes: from left to right, BP of ML, BP of MP, PP of Bayes and BP of NJ. Bootstrap values are reported as percentages. “*” indicates BP = 100% or PP = 1. “-” indicates the node is not recovered by corresponding tree reconstruction method.

**Fig. 2**
The inferred CVTree of the 91 fungi genomes. This tree is obtained using whole-gene repertoires of these genomes with K = 7. Bootstrap values are reported as percentages. “*” indicates BP = 100%. Only higher-than-order level relationships are shown here. See Fig. S14 for the full CVTree.

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[1] Hibbett D.S., Binder M. Evolution of marine mushrooms. Biol Bull. 2001;201:319–322. - PubMed

[2] Hibbett D.S., Binder M. Evolution of marine mushrooms. Biol Bull. 2001;201:319–322. - PubMed

[3] Matheny P.B., Wang Z., Binder M., Curtis J.M., Lim Y.W., Nilsson R.H., Hughes K.W., Hofstetter V., Ammirati J.F., Schoch C.L., Langer E., Langer G., McLaughlin D.J., Wilson A.W., Froslev T., Ge Z.W., Kerrigan R.W., Slot J.C., Yang Z.L., Baroni T.J., Fischer M., Hosaka K., Matsuura K., Seidl M.T., Vauras J., Hibbett D.S. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi) Mol Phylogenetics Evol. 2007;43:430–451. - PubMed

[4] Matheny P.B., Wang Z., Binder M., Curtis J.M., Lim Y.W., Nilsson R.H., Hughes K.W., Hofstetter V., Ammirati J.F., Schoch C.L., Langer E., Langer G., McLaughlin D.J., Wilson A.W., Froslev T., Ge Z.W., Kerrigan R.W., Slot J.C., Yang Z.L., Baroni T.J., Fischer M., Hosaka K., Matsuura K., Seidl M.T., Vauras J., Hibbett D.S. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi) Mol Phylogenetics Evol. 2007;43:430–451. - PubMed

[5] Bruns T.D., Vilgalys R., Barns S.M., Gonzalez D., Hibbett D.S., Lane D.J., Simon L., Stickel S., Szaro T.M., Weisburg W.G. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylogenetics Evol. 1992;1:231–241. - PubMed

[6] Bruns T.D., Vilgalys R., Barns S.M., Gonzalez D., Hibbett D.S., Lane D.J., Simon L., Stickel S., Szaro T.M., Weisburg W.G. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylogenetics Evol. 1992;1:231–241. - PubMed

[7] Lutzoni F., Kauff F., Cox C.J., McLaughlin D., Celio G., Dentinger B., Padamsee M., Hibbett D., James T.Y., Baloch E., Grube M., Reeb V., Hofstetter V., Schoch C., Arnold A.E., Miadlikowska J., Spatafora J., Johnson D., Hambleton S., Crockett M., Shoemaker R., Sung G.H., Lucking R., Lumbsch T., O'Donnell K., Binder M., Diederich P., Ertz D., Gueidan C., Hansen K., Harris R.C., Hosaka K., Lim Y.W., Matheny B., Nishida H., Pfister D., Rogers J., Rossman A., Schmitt I., Sipman H., Stone J., Sugiyama J., Yahr R., Vilgalys R. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 2004;91:1446–1480. - PubMed

[8] Lutzoni F., Kauff F., Cox C.J., McLaughlin D., Celio G., Dentinger B., Padamsee M., Hibbett D., James T.Y., Baloch E., Grube M., Reeb V., Hofstetter V., Schoch C., Arnold A.E., Miadlikowska J., Spatafora J., Johnson D., Hambleton S., Crockett M., Shoemaker R., Sung G.H., Lucking R., Lumbsch T., O'Donnell K., Binder M., Diederich P., Ertz D., Gueidan C., Hansen K., Harris R.C., Hosaka K., Lim Y.W., Matheny B., Nishida H., Pfister D., Rogers J., Rossman A., Schmitt I., Sipman H., Stone J., Sugiyama J., Yahr R., Vilgalys R. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 2004;91:1446–1480. - PubMed

[9] Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf S., James T., Kirk P.M., Lucking R., Thorsten Lumbsch H., Lutzoni F., Matheny P.B., McLaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K.D., Ironside J.E., Koljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schussler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J., Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol Res. 2007;111:509–547. - PubMed

[10] Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf S., James T., Kirk P.M., Lucking R., Thorsten Lumbsch H., Lutzoni F., Matheny P.B., McLaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K.D., Ironside J.E., Koljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schussler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J., Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol Res. 2007;111:509–547. - PubMed

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Resolution of deep divergence of club fungi (phylum Basidiomycota)

Affiliation

Resolution of deep divergence of club fungi (phylum Basidiomycota)

Authors

Affiliation

Erratum in

Abstract

Figures

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Cited by

References

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