Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species

Funding Information: We thank Prof. Jian-Yun Zhuang for his advice on nomenclatural matters. We thank Dr. Alexander Idnurm for his kindly providing the sequences and informations of strain IAM13481 and his critical comments for this manuscript, Dr. Aleksey Kachalkin for his sharing the physilogical data of strain KBP Y-5548 and Masako Takashima for her sharing the physilogical data of strain TY-217. We also thank Ana Pontes and Cl?udia Carvalho for editing illustrations of Kondoa myxariophila and for ITS sequencing, respectively. This study was supported by grants No. 31570016 from the National Natural Science Foundation of China (NSFC) and national project on scientific groundwork No. 2014FY210400 from the Ministry of Science and Technology of China. The authors are solely responsible for the content of this work.Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.publishersversionpublishe

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Funding Information: We want to thank Barbara Roberts from the NCBI Taxonomy Team for providing the update of the current fungal names in NCBI Taxonomic database. Masako Takashima is supported by the Institution for Fermentation, Osaka (IFO). Heide-Marie Daniel is supported by the Belgian Science Policy Office grant C5/00/BCCM. Chris Todd Hittinger is supported by the National Science Foundation under Grant Nos. DEB-1442148 and DEB-2110403, the USDA National Institute of Food and Agriculture (Hatch Project 1020204), in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE–SC0018409, and an H.I. Romnes Faculty Fellowship, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in Antonis Rokas’s lab is supported by grants from the National Science Foundation (DEB-1442113 and DEB-2110404), the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. Antonis Rokas acknowledges support from a Klaus Tschira Guest Professorship from the Heidelberg Institute for Theoretical Studies and from a Visiting Research Fellowship from Merton College of the University of Oxford. Marc-André Lachance acknowledges lifelong financial support from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Carlos A. Rosa is supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – Brazil, process numbers 408733/2021-7 and 406564/2022-1); Fundação do Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG, process numberAPQ-01525-14). Teun Boekhout is supported by the Distinguished Scientist Fellow Program of King Saud University, Ryadh, Saudi Arabia. Publisher Copyright: © 2023 Westerdijk Fungal Biodiversity Institute.The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.publishersversionpublishe

Derxomyces napiformis Q. M. Wang, F. Y. Bai & A. H. Li 2020, sp. nov.

<p> <i>Derxomyces napiformis</i> Q.M. Wang, F.Y. Bai & A.H. Li <i>sp. nov.</i> MycoBank MB828775. Fig. 9K, L.</p> <p> <i>Etymology</i>: the specific epithet <i>napiformis</i> refers to the napiform ballistoconidia of the type strain.</p> <p> <i>Culture characteristics</i>: In YM broth, after 7 d at 17 °C, cells are ellipsoidal to ovoid, 1.5– 4.3 × 5.0–8.6 μm and single, budding is polar (Fig. 9K), a sediment is formed. After 1 mo at 17 °C, a ring and sediment are present. On YM agar, after 1 mo at 17 °C, the streak culture is yellowish-cream, butyrous, slightly wrinkled and dull. The margin is entire. In Dalmau plate culture on corn meal agar, pseudohyphae are formed. Sexual structures are not observed on YM, PDA, V8 and CM agar. Ballistoconidia are ellipsoidal to napiform, 2.9– 3.6 × 4.2– 4.6 μm (Fig. 9L).</p> <p> <i>Physiological and biochemical characteristics</i>: Glucose fermentation is absent. Glucose, galactose, sucrose, maltose, cellobiose, trehalose, melibiose, raffinose, melezitose, D-xylose, Larabinose, D-arabinose, L-rhamnose, Methyl-α- D-glucoside, succinate and myo-inositol are assimilated as sole carbon sources. L-sorbose, lactose, inulin, soluble starch, D-ribose, Dglucosamine, methanol, ethanol, glycerol, erythritol, ribitol, galactitol, D-mannitol, D-glucitol, salicin, DL-lactate, citrate and hexadecane are not assimilated. Ammonium sulfate, L-lysine, ethylamine hydrochloride and cadaverine dihydrochloride are assimilated as sole nitrogen sources. Potassium nitrate and sodium nitrite are not assimilated. Maximum growth temperature is 28 °C. Growth in vitamin-free medium is negative. Starch-like substances are not produced. Growth on 50 % (w/w) glucose-yeast extract agar is negative. Urease activity is positive. Diazonium Blue B reaction is positive.</p> <p> Physiologically, <i>De. napiformis</i> differs from its closely related species <i>De. bifurcus</i> in its inability to assimilate inulin, D-ribose and potassium nitrate and its ability to assimilate Methyl-α- Dglucoside, succinate and myo-inositol (Table S1.11).</p> <p> <i>Typus</i>: <b>China</b>, Taiwan province, obtained from a leaf of an unidentified plant, Aug. 2009, Q.-M. Wang (<b>holotype</b> CGMCC 2.4446 T preserved in a metabolically inactive state, ex-type CBS 15748 = TW1.1F028).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 95, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Derxomyces cylindricus F. Y. Bai & Q. M. Wang 2020, sp. nov.

<p> <i>Derxomyces cylindricus</i> F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang, <i>sp. nov.</i> MycoBank MB831863.</p> <p>For description see Int. J. Syst. Evol. Microbiol. 54(5): 1879 (2004).</p> <p> <i>Holotype:</i> CGMCC AS 2.2308 (preserved in a metabolically inactive state).</p> <p> <i>Synonyms</i>: <i>Bullera cylindrica</i> F.Y. Bai, Q.M. Wang & M. Takash., Int. J. Syst. Evol. Microbiol. 54(5): 1879 (2004), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p> <p> = <i>Derxomyces cylindrica</i> F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang, FEMS Yeast Res. 8(5): 804 (2008), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 133, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Derxomyces nakasei F. Y. Bai & Q. M. Wang 2020, sp. nov.

<p> <i>Derxomyces nakasei</i> F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang, <i>sp. nov.</i> MycoBank MB831865.</p> <p>For description see Int. J. Syst. Evol. Microbiol. 54(5): 1880 (2004).</p> <p> <i>Holotype:</i> CGMCC AS 2.2435 (preserved in a metabolically inactive state).</p> <p> <i>Synonyms</i>: <i>Bullera nakasei</i> F.Y. Bai, Q.M. Wang & M. Takash., Int. J. Syst. Evol. Microbiol. 54(5): 1880 (2004), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p> <p> = <i>Derxomyces nakasei</i> F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang, FEMS Yeast Res. 8(5): 805 (2008), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 133, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Derxomyces ovatus Q. M. Wang, F. Y. Bai & A. H. Li 2020, sp. nov.

<p> <i>Derxomyces ovatus</i> Q.M. Wang, F.Y. Bai & A.H. Li <i>sp. nov.</i> MycoBank MB828780. Fig. 10E, F.</p> <p> <i>Etymology</i>: the specific epithet <i>ovatus</i> refers to the ovoid vegetative cells of the type strain.</p> <p> <i>Culture characteristics</i>: In YM broth, after 7 d at 17 °C, cells are ovoid or ellipsoidal, 2.0– 5.4 × 3.8– 7.7 μm and single, budding is polar (Fig. 10E), a sediment is present. After 1 mo at 17 °C, a ring and a sediment are present. On YM agar, after 1 mo at 17 °C, the streak culture is yellow, butyrous, smooth and dull. The margin is entire. In Dalmau plate culture on corn meal agar, pseudohyphae are formed. Sexual structures are not observed on YM, PDA, V8 and CM agar. Ballistoconidia are ellipsoidal to napiform, 1.8 –3.6 × 3.0–4.5 μm (Fig. 10F).</p> <p> <i>Physiological and biochemical characteristics</i>: Glucose fermentation is absent. Glucose, galactose, L-sorbose (delayed and weak), sucrose, maltose, cellobiose, trehalose, melibiose, raffinose, melezitose, inulin (delayed and weak), soluble starch (weak), D-xylose, Larabinose, L-rhamnose, ethanol (delayed and weak), galactitol, Dmannitol, D-glucitol, Methyl-α- D-glucoside, salicin (delayed and weak), succinate and myo-inositol are assimilated as sole carbon sources. Lactose, D-arabinose, D-ribose, D-glucosamine, N-Acetyl-D-glucosamine, methanol, glycerol, erythritol, ribitol, DL-lactate, citrate and hexadecane are not assimilated. Ammonium sulfate, potassium nitrate (delayed and weak) and L-lysine are assimilated as sole nitrogen sources. Sodium nitrite, ethylamine hydrochloride and cadaverine dihydrochloride are not assimilated. Maximum growth temperature is 28 °C. Growth in vitamin-free medium is netative. Starch-like substances are not produced. Growth on 50 % (w/w) glucose-yeast extract agar is negative. Urease activity is positive. Diazonium Blue B reaction is positive.</p> <p> Physiologically, <i>De. ovatus</i> differs from the closely related species <i>De. taiwanicus</i>. in its ability to assimilate myo-inositol (Table S1.11).</p> <p> <i>Typus</i>: <b>China</b>, Simao county, Yunnan province, obtained from a leaf of an unidentified plant, Nov. 2006, Q.-M. Wang (<b>holotype</b> CGMCC 2.3572 T preserved in a metabolically inactive state, ex-type CBS 15654 = SM32.2).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 98, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Derxomyces longiovatus Q. M. Wang, F. Y. Bai & A. H. Li 2020, sp. nov.

<p> <i>Derxomyces longiovatus</i> Q.M. Wang, F.Y. Bai & A.H. Li <i>sp. nov.</i> MycoBank MB828774. Fig. 9I, J.</p> <p> <i>Etymology</i>: the specific epithet <i>longiovatus</i> refers to the long ovoid vegetative cells of the type strain.</p> <p> <i>Culture characteristics</i>: In YM broth, after 7 d at 17 °C, cells are long ovoid, cylindrical and ellipsoidal, 1.8– 3.7 × 3.9– 13.8 μm and single, budding is polar (Fig. 9I), a sediment is formed. After 1 mo at 17 °C, a pellicle and sediment are present. On YM agar, after 1 mo at 17 °C, the streak culture is yellowish-cream, butyrous, dull. The margin is entire or eroded. In Dalmau plate culture on corn meal agar, pseudohyphae and hyphaeare formed. Sexual structures are not observed on YM, PDA, V8 and CM agar. Ballistoconidia are subglobosal to napiform, 3.2–4.5 × 4.8– 6.5 μm (Fig. 9J).</p> <p> <i>Physiological and biochemical characteristics</i>: Glucose fermentation is absent. Glucose, galactose, sucrose, maltose, cellobiose (delayed and weak), trehalose, melibiose, raffinose, melezitose, inulin, soluble starch, D-xylose, L-arabinose, Darabinose, L-rhamnose (delayed and weak), salicin (delayed and weak) and myo-inositol (weak) are assimilated as sole carbon sources. L-sorbose, lactose, D-ribose, D-glucosamine, N-Acetyl-D-glucosamine, methanol, ethanol, glycerol, erythritol, ribitol, galactitol, D-mannitol, D-glucitol, Methyl-α- D-glucoside, DLlactate, succinate, citrate and hexadecane are not assimilated. Ammonium sulfate, potassium nitrate, L-lysine, ethylamine hydrochloride, cadaverine dihydrochloride are assimilatedas sole nitrogen sources. Sodium nitrite is not assimilated. Maximum growth temperature is 28 °C. Growth in vitamin-free medium is negative. Starch-like substances are not produced. Growth on 50 % (w/w) glucose-yeast extract agar is negative. Urease activity is positive. Diazonium Blue B reaction is positive.</p> <p> Physiologically, <i>De. longiovatus</i> and its closely related species <i>De. pseudoyunnanensis</i> as well as <i>De. yunnanensis</i> are very similar. The two new species are not distinguishable, they differ from <i>De. yunnanensis</i> in its ability to assimilate inulin (Table S1.11).</p> <p> <i>Typus</i>: <b>China</b>, Simao county, Yunnan province, obtained from a leaf of an unidentified plant, Nov. 2006, Q.-M. Wang (<b>holotype</b> CGMCC 2.3535 T preserved in a metabolically inactive state, ex-type CBS 15659 = SM35.4).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on pages 94-95, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Oberwinklerozyma straminea Q. M. Wang, F. Y. Bai, M. Groenew. & Boekhout 2020, sp. nov.

<p> <i>Oberwinklerozyma straminea</i> Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout, <i>sp. nov.</i> MycoBank MB831744.</p> <p>For description see Int. J. Syst. Evol. Microbiol. 60(10): 2505 (2010).</p> <p> <i>Holotype:</i> CBS 10976 (preserved in a metabolically inactive state).</p> <p> <i>Synonyms</i>: <i>Rhodotorula straminea</i> Golubev & Scorzetti, Int. J. Syst. Evol. Microbiol. 60(10): 2505 (2010), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p> <p> = <i>Oberwinklerozyma straminea</i> Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout, Stud. Mycol. 81: 185 (2015), <i>nom. inval.</i>, Art. 40.7 (Shenzhen).</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 135, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt

Teunia Q. M. Wang & F. Y. Bai 2020, gen. nov.

<p> <i>Teunia</i> Q.M. Wang & F.Y. Bai <i>gen. nov.</i> MycoBank MB828751.</p> <p> <i>Etymology</i>: the genus is named in honour of Dr. Teun Boekhout for his contributions to yeast taxonomy.</p> <p> This genus is proposed for the clade represented by <i>Cryptococcus cuniculi</i>, which clustered with <i>Fonsecazyma tronadorensis</i> (<i>Cryptococcus tronadorensis</i>), <i>Fonsecazyma betulae</i> (<i>Kwoniella betulae</i>) and three new species represented by CGMCC 2.4450, CGMCC 2.5648 and CGMCC 2.3835, respectively. Member of the <i>Cryptococcaceae</i> (<i>Tremellales</i>). The genus is mainly circumscribed by the phylogenetic analysis of the seven genes dataset, in which it occurred as a well supported clade within <i>Cryptococcaceae</i> (Fig. 2).</p> <p>Sexual reproduction not known. Colonies cream to yellow, butyrous to mucoid. Budding cells present. Pseudohyphae and hyphae are not produced. Ballistoconidia are not formed.</p> <p> <i>Type species</i>: <i>Teunia korlaensis</i> Q.M. Wang, F.Y. Bai & A.H. Li.</p>Published as part of <i>Li, A. - H., Yuan, F. - X., Groenewald, M., Bensch, K., Yurkov, A. M., Li, K., Han, P. - J., Guo, L. - D., Aime, M. C., Sampaio, J. P., Jindamorakot, S., Turchetti, B., Inacio, J., Fungsin, B., Wang, Q. - M. & Bai, F. - Y., 2020, Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species, pp. 17-140 in Studies In Mycology 96</i> on page 86, DOI: 10.1016/j.simyco.2020.01.002, <a href="http://zenodo.org/record/10497182">http://zenodo.org/record/10497182</a&gt