Description of the New Species Laccaria albifolia (Hydnangiaceae, Basidiomycota) and a Reassessment of Laccaria affinis Based on Morphological and Phylogenetic Analyses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Morphology
2.2. Molecular Phylogeny
2.3. Sequence Alignment, Dataset Assembly and Phylogenetic Analysis
3. Results
3.1. Molecular Phylogeny
3.2. Taxonomy
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Kirk, P.; Cannon, P.; Minter, D.; Stalpers, J. Ainsworth and Bisby’s Dictionary of the Fungi, 10th ed.; CABI Publishing: Wallingford, UK, 2008; ISBN 978-0-85199-826-8. [Google Scholar]
- Mueller, G.M. Systematics of Laccaria (Agaricales) in the continental United States and Canada, with discussions on extralimital taxa and descriptions of extant types. Fieldiana Bot. 1992, 30, 1–158. [Google Scholar]
- He, M.Q.; Zhao, R.L.; Hyde, K.D.; Begerow, D.; Kemler, M.; Yurkov, A.; McKenzie, E.H.C.; Raspé, O.; Kakishima, M.; Sánchez-Ramírez, S.; et al. Notes, outline and divergence times of Basidiomycota. Fungal Divers. 2019, 99, 105–367. [Google Scholar] [CrossRef]
- Cho, H.J.; Lee, H.; Park, M.S.; Park, K.H.; Park, J.H.; Cho, Y.; Kim, C.; Lim, Y.W. Two new species of Laccaria (Agaricales, Basidiomycota) from Korea. Mycobiology 2020, 48, 1786961. [Google Scholar] [CrossRef]
- Corrales, A.; Wilson, A.W.; Mueller, G.M.; Ovrebo, C. Novel Laccaria Species from Juglandaceae Forest in Panama With Notes on Their Ecology. Front. Microbiol. 2020, 11, 1597. [Google Scholar] [CrossRef]
- Li, F. Two new species of Laccaria from South China, with a note on Hodophilus glaberipes. Mycol. Prog. 2020, 19, 525–539. [Google Scholar] [CrossRef]
- Zhang, M.; Gao, X.-L.; Mu, L.-Q.; Deng, W.-Q. Morphology and Molecular Phylogeny Reveal Five New Species of Laccaria (Hydnangiaceae, Agaricales) from Southern China. J. Fungi 2023, 9, 1179. [Google Scholar] [CrossRef]
- Singer, R. Notes sur le genre Laccaria. Bull. Trimest. Soc. Mycol. Fr. 1967, 83, 104–123. [Google Scholar]
- Bon, M. Tricholomataceae de Franee et d’Europe oeeidentale. Clé Monogr. Doc. Mycol. 1983, 51, 1–51. [Google Scholar]
- Migliozzi, V.; Lavorato, C. Appunti di micoflora mediterranea. 6. Laccaria affinis fo. macrocystidiata fo. nov. Micol. Ital. 1988, 17, 3–6. [Google Scholar]
- Pázmány, D. Zur Systematik der Gattung Laccaria Bk. et Br. Z. Mykol. 1994, 60, 5–12. [Google Scholar]
- Contu, M. Il genere Laccaria (Basidiomycotina, Agaricales) in Italia, con note sulle rimanenti specie in Europa. Boll. Gr. Micol. Bresadola 2003, 46, 5–58. [Google Scholar]
- Dovana, F.; Moreno, G.; Para, R.; Lavorato, C.; Mucciarelli, M. Phylogenetic reappraisal and epitypification of Laccaria macrocystidiata (Hydnangiaceae, Basidiomycota). Phytotaxa 2021, 514, 129–139. [Google Scholar] [CrossRef]
- Osmundson, T.W.; Cripps, C.L.; Mueller, G.M. Morphological and molecular systematics of Rocky Mountain alpine. Laccaria Mycologia 2005, 997, 949–972. [Google Scholar] [CrossRef]
- Wilson, A.W.; Hosaka, K.; Mueller, G. Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus. Laccaria New Phytol. 2017, 213, 1862–1873. [Google Scholar] [CrossRef] [PubMed]
- Moreno, G.; Castillo, A.; Thüs, H. Critical revision of type material of Stemonitales (Myxogastria) at the Natural History Museum London (BM). Phytotaxa 2018, 344, 149–159. [Google Scholar] [CrossRef]
- Doyle, J.J.; Doyle, J.L. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem. Bull. 1987, 19, 11–15. [Google Scholar]
- Osmundson, T.W.; Eyre, C.A.; Hayden, K.M.; Dhillon, J.; Garbelotto, M.M. Back to basics: An evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples. Mol. Ecol. Resour. 2013, 13, 66–74. [Google Scholar] [CrossRef]
- White, T.J.; Bruns, T.D.; Lee, S.B.; Taylor, J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications; Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J., Eds.; Academic Press: New York, NY, USA, 1990; pp. 315–322. [Google Scholar]
- Gardes, M.; Bruns, T.D. ITS primers with enhanced specificity for basidiomycetes—Application to the identification of mycorrhizae and rusts. Mol. Ecol. 1993, 2, 113–118. [Google Scholar] [CrossRef]
- Vilgalys, R.; Hester, M. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 1990, 172, 4238–4246. [Google Scholar] [CrossRef]
- Matheny, P.B. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe, Agaricales). Mol. Phylogenet. Evol. 2005, 35, 1–20. [Google Scholar] [CrossRef]
- Rehner, S.A.; Buckley, E.A. Beauveria phylogeny inferred from nuclear ITS and EF1-a sequences: Evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 2005, 97, 84–98. [Google Scholar] [CrossRef] [PubMed]
- Sheedy, E.M.; Van de Wouw, A.P.; Howlett, B.J.; May, T.W. Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia. Mycologia 2013, 105, 547–563. [Google Scholar] [CrossRef] [PubMed]
- Garbelotto, M.; Johnson, M.G. High-Throughput DNA Metabarcoding of Stem Sections from Trees with Cavities Describes Fungal Communities Associated with Variable Wood Decay, Position on Stem and Tree Species. Forests 2023, 14, 1070. [Google Scholar] [CrossRef]
- Callahan, B.J.; McMurdie, P.J.; Rosen, M.J.; Han, A.W.; Johnson, A.J.A.; Holmes, S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 2016, 13, 581–583. [Google Scholar] [CrossRef]
- Abarenkov, K.; Nilsson, R.H.; Larsson, K.-H.; Taylor, A.F.S.; May, T.W.; Frøslev, T.G.; Pawlowska, J.; Lindahl, B.; Põldmaa, K.; Truong, C.; et al. The UNITE Database for Molecular Identification and Taxonomic Communication of Fungi and Other Eukaryotes: Sequences, Taxa and Classifications Reconsidered. Nucleic Acids Res. 2024, 52, D791–D797. [Google Scholar] [CrossRef]
- Zhang, Y.; Park, C.; Bennett, C.; Thornton, M.; Kim, D. Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N. Genome Res. 2021, 31, 1290–1295. Available online: https://www.genome.org/cgi/doi/10.1101/gr.275193.120 (accessed on 1 August 2024). [CrossRef]
- Danecek, P.; Bonfield, J.K.; Liddle, J.; Marshall, J.; Ohan, V.; Pollard, M.O.; Whitwham, A.; Keane, T.; McCarthy, S.H.; Davies, R.M.; et al. Twelve years of SAMtools and BCFtools. Gigascience 2021, 10, giab008. [Google Scholar] [CrossRef]
- Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28, 1647–1649. [Google Scholar] [CrossRef]
- Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403–410. [Google Scholar] [CrossRef]
- Katoh, K.; Toh, H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 2008, 9, 286–298. [Google Scholar] [CrossRef]
- Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [PubMed]
- Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.F.K.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef] [PubMed]
- Hoang, D.T.; Chernomor, O.; von Haeseler, A.; Minh, B.Q.; Le Vinh, S. UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 2018, 35, 518–522. [Google Scholar] [CrossRef] [PubMed]
- Ronquist, F.; Huelsenbeck, J.P.; Teslenko, M. MrBayes Version 3.2 Manual: Tutorials and Model Summaries. 2011. Available online: https://gensoft.pasteur.fr/docs/mrbayes/3.2.7/Manual_MrBayes_v3.2.pdf (accessed on 19 October 2021).
- Miller, M.A.; Pfeiffer, W.; Schwartz, T. Creating the cipres science gateway for inference of large phylogenetic trees. In Proceedings of the 2010 Gateway Computing Environments Workshop (GCE), New Orleans, LA, USA, 14 November 2010; IEEE: Manhattan, NY, USA, 2010. [Google Scholar]
- Lanfear, R.; Frandsen, P.B.; Wright, A.M.; Senfeld, T.; Calcott, B. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol. Biol. Evol. 2016, 34, 772–773. [Google Scholar] [CrossRef]
- Wilson, A.W.; Hosaka, K.; Perry, B.A.; Mueller, G.M. Laccaria (Agaricomycetes, Basidiomycota) from Tibet (Xizang Autonomous Region, China). Mycoscience 2013, 54, 406–419. [Google Scholar] [CrossRef]
- Wilson, A.W.; Wickett, N.J.; Grabowski, P.; Fant, J.; Borevitz, J.; Mueller, G.M. Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology. Mycologia 2015, 107, 217–226. [Google Scholar] [CrossRef]
- Ben Ali, M.B.H.; Boekhout, T.; Thorn, R.G. Assemblages of fungi associated with cork oak forests in northwestern Tunisia. Nova Hedwig. 2017, 105, 121–134. [Google Scholar] [CrossRef]
- Zimmer, K.; Hynson, N.A.; Gebauer, G.; Allen, E.B.; Allen, M.F.; Read, D.J. Wide geographical and ecological distribution of nitrogen and carbon gains from fungi in pyroloids and monotropoids (Ericaceae) and in orchids. New Phytol. 2007, 175, 166–175. [Google Scholar] [CrossRef]
- Vincenot, L.; Nara, K.; Sthultz, C.; Labbé, J.; Dubois, M.P.; Tedersoo, L.; Martin, F.; Selosse, M.A. Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex. Mol. Ecol. 2012, 21, 281–299. [Google Scholar] [CrossRef] [PubMed]
- Kjøller, R. Disproportionate abundance between ectomycorrhizal root tips and their associated mycelia. FEMS Microbiol. Ecol. 2006, 58, 214–224. [Google Scholar] [CrossRef]
- Suz, L.M.; Barsoum, N.; Benham, S.; Dietrich, H.P.; Fetzer, K.D.; Fischer, R.; García, P.; Gehrman, J.; Kristöfel, F.; Manninger, M. Environmental drivers of ectomycorrhizal communities in Europe’s temperate oak forests. Mol. Ecol. 2014, 23, 5628–5644. [Google Scholar] [CrossRef] [PubMed]
- Ważny, R. Ectomycorrhizal communities associated with silver fir seedlings (Abies alba Mill.) differ largely in mature silver fir stands and in Scots pine forecrops. Ann. For. Sci. 2014, 71, 801–810. [Google Scholar] [CrossRef]
- De Witte, L.C.; Rosenstock, N.P.; Van Der Linde, S.; Braun, S. Nitrogen deposition changes ectomycorrhizal communities in Swiss beech forests. Sci. Total Environ. 2017, 605–606, 1083–1096. [Google Scholar] [CrossRef]
- Hofstetter, V.; Buyck, B.; Eyssartier, G.; Schnee, S.; Gindro, K. The unbearable lightness of sequenced-based identification. Fungal Divers. 2019, 96, 243–284. [Google Scholar] [CrossRef]
- Lang, C.; Seven, J.; Polle, A. Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed central European forest. Mycorrhiza 2011, 21, 297–308. [Google Scholar] [CrossRef]
- Cho, H.J.; Park, M.S.; Lee, H.; Oh, S.Y.; Wilson, A.W.; Mueller, G.M.; Lim, Y.W. A systematic revision of the ectomycorrhizal genus Laccaria from Korea. Mycologia 2018, 110, 948–961. [Google Scholar] [CrossRef]
- Buscardo, E.; Rodríguez-Echeverría, S.; Martín, M.P.; De Angelis, P.; Pereira, J.S.; Freitas, H. Impact of wildfire return interval on the ectomycorrhizal resistant propagules communities of a Mediterranean open forest. Fungal Biol. 2010, 114, 628–636. [Google Scholar] [CrossRef]
- Branco, S.; Ree, R.H. Serpentine Soils Do Not Limit Mycorrhizal Fungal Diversity. PLoS ONE 2010, 5, e11757. [Google Scholar] [CrossRef]
- López-García, Á.; Gil-Martínez, M.; Navarro-Fernández, C.M.; Kjøller, R.; Azcón-Aguilar, C.; Domínguez, M.T.; Marañón, T. Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination. Soil Biol. Biochem. 2018, 121, 202–211. [Google Scholar] [CrossRef]
- Popa, F.; Rexer, K.H.; Donges, K.; Yang, Z.L.; Kost, G. Three new Laccaria species from Southwest China (Yunnan). Mycol. Prog. 2014, 13, 1105–1117. [Google Scholar] [CrossRef]
- Crous, P.W.; Osieck, E.R.; Jurjevi, Ž.; Boers, J.; Van Iperen, A.L.; Starink-Willemse, M.; Dima, B.; Balashov, S.; Bulgakov, T.S.; Johnston, P.R.; et al. Fungal Planet description sheets: 1284–1382. Persoonia 2021, 47, 178–374. [Google Scholar] [CrossRef] [PubMed]
- Cui, Y.Y.; Cai, Q.; Li, J.; Yang, Z.L. Two new Laccaria species from China based on molecular and morphological evidence. Mycol. Prog. 2021, 20, 567–576. [Google Scholar] [CrossRef]
- Wang, X.H.; Das, K.; Bera, I.; Chen, Y.H.; Bhatt, R.P.; Ghosh, A.; Hembrom, M.E.; Hofdtetter, V.; Parihar, A.; Vizzini, A.; et al. Fungal Biodiversity Profiles 81–90. Cryptogam. Mycol. 2019, 40, 57–95. [Google Scholar] [CrossRef]
- Vincenot, L.; Popa, F.; Laso, F.; Donges, K.; Rexer, K.H.; Kost, G.; Yang, Z.L.; Nara, K.; Selosse, M.A. Out of Asia: Biogeography of fungal populations reveals Asian origin of diversification of the Laccaria amethystina complex, and two new species of violet Laccaria. Fungal Biol. 2017, 121, 939–955. [Google Scholar] [CrossRef]
- Armada, F.; Bellanger, J.-M.; Moreau, P.-A. Champignons de la Zone Alpine; Fédération Mycologique et Botanique Dauphiné-Savoie: Annemasse, France, 2023; pp. 1–376. [Google Scholar]
- Boonmee, S.; Wanasinghe, D.N.; Calabon, M.S.; Huanraluek, N.; Chandrasiri, S.K.U.; Jones, G.E.B.; Rossi, W.; Leonardi, M.; Singh, S.K.; Rana, S.; et al. Fungal diversity notes 1387–1511: Taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Divers. 2021, 111, 1–335. [Google Scholar] [CrossRef]
- Montoya, L.; Bandala, V.M.; Baroni, T.J.; Horton, T.R. A new species of Laccaria in montane cloud forest from eastern Mexico. Mycoscience 2015, 56, 597–605. [Google Scholar] [CrossRef]
- Luo, X.; Ye, L.; Chen, J.; Karunarathna, S.C.; Xu, J.C.; Hyde, K.D.; Mortimer, P.E. Laccaria rubroalba sp. nov. (Hydnangiaceae, Agaricales) from Southwestern China. Phytotaxa 2016, 284, 41–50. [Google Scholar] [CrossRef]
- Ramos, A.; Bandala, V.M.; Montoya, L. A new species and a new record of Laccaria (Fungi, Basidiomycota) found in a relict forest of the endangered Fagus grandifolia var. mexicana. MycoKeys 2017, 27, 77–94. [Google Scholar] [CrossRef]
- Popa, F.; Jimenéz, S.Y.C.; Weisenborn, J.; Donges, K.; Rexer, K.H.; Piepenbring, M. A new Laccaria species from cloud forest of Fortuna, Panama. Mycol. Prog. 2016, 15, 19. [Google Scholar] [CrossRef]
- Cortese, A.M.; Horton, T.R. Ectomycorrhizal tree islands in arbuscular mycorrhizalforests: Hotspots of fungal inoculum important for seedlingestablishment of historically dominant trees. J. Ecol. 2024, 112, 2680–2694. [Google Scholar] [CrossRef]
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Dovana, F.; Para, R.; Moreno, G.; Scali, E.; Garbelotto, M.; Lechner, B.E.; Forte, L. Description of the New Species Laccaria albifolia (Hydnangiaceae, Basidiomycota) and a Reassessment of Laccaria affinis Based on Morphological and Phylogenetic Analyses. J. Fungi 2025, 11, 11. https://doi.org/10.3390/jof11010011
Dovana F, Para R, Moreno G, Scali E, Garbelotto M, Lechner BE, Forte L. Description of the New Species Laccaria albifolia (Hydnangiaceae, Basidiomycota) and a Reassessment of Laccaria affinis Based on Morphological and Phylogenetic Analyses. Journal of Fungi. 2025; 11(1):11. https://doi.org/10.3390/jof11010011
Chicago/Turabian StyleDovana, Francesco, Roberto Para, Gabriel Moreno, Edoardo Scali, Matteo Garbelotto, Bernardo Ernesto Lechner, and Luigi Forte. 2025. "Description of the New Species Laccaria albifolia (Hydnangiaceae, Basidiomycota) and a Reassessment of Laccaria affinis Based on Morphological and Phylogenetic Analyses" Journal of Fungi 11, no. 1: 11. https://doi.org/10.3390/jof11010011
APA StyleDovana, F., Para, R., Moreno, G., Scali, E., Garbelotto, M., Lechner, B. E., & Forte, L. (2025). Description of the New Species Laccaria albifolia (Hydnangiaceae, Basidiomycota) and a Reassessment of Laccaria affinis Based on Morphological and Phylogenetic Analyses. Journal of Fungi, 11(1), 11. https://doi.org/10.3390/jof11010011