The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102: 95-132. doi: 10.3114/sim.2022.102.03.

BCCM IHEM collection Mycology and Aerobiology Sciensano Bruxelles Belgium

Biological Resource Center National Institute of Technology and Evaluation Kisarazu Japan

Department of Biochemistry Genetics and Microbiology Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa

Department of Botany Faculty of Science Charles University Prague Czech Republic

Graduate School of Medical and Pharmaceutical Sciences Chiba University Chiba Japan

Laboratory of Fungal Genetics and Metabolism Institute of Microbiology Czech Academy of Sciences Prague Czech Republic

Medical Mycology Research Center Chiba University Chiba Japan

Molecular Chirality Research Center Chiba University Chiba Japan

Plant Molecular Science Center Chiba University Chiba Japan

Westerdijk Fungal Biodiversity Institute Utrecht the Netherlands

Zobrazit více v PubMed

Ahrens D, Fujisawa T, Krammer H-J, PubMed

Alcazar-Fuoli L, Mellado E, Alastruey-Izquierdo A, PubMed PMC

Al-Musallam (1980). A revision of the black Aspergillus species. Ph.D. dissertation. Rijksuniversiteit; Utrecht, Netherlands.

Andersen MR, Salazar MP, Schaap PJ, PubMed PMC

Bairoch A, Apweiler R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28: 45–48. PubMed PMC

Ban S, Kasaishi R, Kamijo T, PubMed PMC

Bankevich A, Nurk S, Antipov D, PubMed PMC

Bennett JW, Klich MA. (1992). Aspergillus: biology and industrial applications. Butterworth-Heinemann, USA.

Boluda CG, Rico VJ, Divakar PK, PubMed PMC

Bouckaert R, Heled J, Kühnert D, PubMed PMC

Buchfink B, Xie C, Huson DH. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods 12: 59–60. PubMed

Carstens BC, Pelletier TA, Reid NM, Satler JD. (2013). How to fail at species delimitation. Molecular Ecology 22: 4369–4383. PubMed

Cerqueira GC, Arnaud MB, Inglis DO, PubMed PMC

Chambers EA, Hillis DM. (2020). The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology 69: 184–193. PubMed

Chen Y, Nie F, Xie S-Q, PubMed PMC

Crous PW, Verkley GJM, Groenewald JZ,

de Vries RP, Riley R, Wiebenga A, PubMed PMC

Dettman JR, Jacobson DJ, Taylor JW. (2003a). A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote PubMed

Dettman JR, Jacobson DJ, Turner E, PubMed

D’hooge E, Becker P, Stubbe D, PubMed

Donaldson GC, Ball LA, Axelrood PE, PubMed PMC

Dyer PS, O’Gorman CM. (2011). A fungal sexual revolution: PubMed

Ellena V, Seekles SJ, Vignolle GA, PubMed PMC

Emms DM, Kelly S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20: 238. PubMed PMC

Feng X, Wang X, Chiang Y,

Frisvad JC, Larsen TO, Thrane U, PubMed PMC

Frisvad JC, Møller LLH, Larsen TO, PubMed PMC

Frisvad JC, Petersen LM, Lyhne EK, PubMed PMC

Fungaro MHP, Ferranti LS, Massi FP, PubMed PMC

Gams W, Christensen M, Onions AH,

Gautier M, Normand A-C, Ranque S. (2016). Previously unknown species of PubMed

Gits-Muselli M, Hamane S, Verillaud B, PubMed

Glässnerová K, Sklenář F, Jurjević Ž, PubMed PMC

Gnerre S, MacCallum I, Przybylski D, PubMed PMC

Grüning B, Dale R, Sjödin A, PubMed PMC

Hashimoto A, Hagiwara D, Watanabe A, PubMed PMC

Heled J, Drummond AJ. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27: 570–580. PubMed PMC

Hendrickx M, Beguin H, Detandt M. (2012). Genetic re-identification and antifungal susceptibility testing of PubMed

Hilário S, Gonçalves MFM, Alves A. (2021). Using genealogical concordance and coalescent-based species delimitation to assess species boundaries in the PubMed PMC

Hong S-B, Cho HS, Shin HD, PubMed

Hong S-B, Lee M, Kim DH, PubMed PMC

Hong S-B, Yamada O, Samson RA. (2014). Taxonomic re-evaluation of black koji molds. Applied Microbiology and Biotechnology 98: 555–561. PubMed

Horn BW, Olarte RA, Peterson SW, PubMed

Houbraken J, de Vries RP, Samson RA. (2014). Modern taxonomy of biotechnologically important PubMed

Houbraken J, Kocsubé S, Visagie CM, PubMed PMC

Howard SJ, Harrison E, Bowyer P, PubMed PMC

Hubka V, Barrs V, Dudová Z, PubMed PMC

Hubka V, Kolarik M. (2012). β-tubulin paralogue PubMed PMC

Hubka V, Kubatova A, Mallatova N, PubMed

Huerta-Cepas J, Szklarczyk D, Forslund K, PubMed PMC

Ismail MA. (2017). Incidence and significance of black aspergilli in agricultural commodities: a review, with a key to all species accepted to-date. European Journal of Biological Research 7: 207–222.

Jin JJ, Yu W bin, Yang JB, PubMed PMC

Jones G. (2017). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology 74: 447–467. PubMed

Jones G, Aydin Z, Oxelman B. (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31: 991–998. PubMed

Jones P, Binns D, Chang HY, PubMed PMC

Jurjević Ž, Peterson SW, Stea G, PubMed PMC

Jurjević Ž, Kubátová A, Kolařík M, Hubka V. (2015). Taxonomy of

Katoh K, Rozewicki J, Yamada KD. (2019). MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. PubMed PMC

Khuna S, Suwannarach N, Kumla J, PubMed PMC

Kocsubé S, Perrone G, Magistà D, PubMed PMC

Korf I. (2004). Gene finding in novel genomes. BMC Bioinformatics 5: 59. PubMed PMC

Kozakiewicz Z. (1989).

Kozakiewicz Z, Frisvad JC, Hawksworth DL, Pitt JI, Samson RA, Stolk AC. (1992). Proposal for

Krueger F. (2015). Trim Galore!: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects.

Kubatko LS, Degnan JH. (2007). Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 17–24. PubMed

Kück P, Mayer C, Wägele J-W, PubMed PMC

Kundu R, Casey J, Sung WK. (2019). HyPo: super fast & accurate polisher for long read genome assemblies. bioRxiv doi: 10.1101/2019.12.19.882506. DOI

Kusters-van Someren MA, Samson RA, Visser J. (1991). The use of RFLP analysis in classification of the black Aspergilli: reinterpretation of the

Lanfear R, Frandsen PB, Wright AM, PubMed

Letunic I, Bork P. (2021). Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49: W293–W296. PubMed PMC

Li H, Durbin R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. PubMed PMC

Li H, Handsaker B, Wysoker A, PubMed PMC

Li Y, Wen J, Ren Y,

Liu YJ, Whelen S, Hall BD. (1999). Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution 16: 1799–1808. PubMed

Mageswari A, Kim J, Cheon K-H, PubMed PMC

Majoros WH, Pertea M, Salzberg SL. (2004). TigrScan and GlimmerHMM: two open source PubMed

Matute DR, Sepúlveda VE. (2019). Fungal species boundaries in the genomics era. Fungal Genetics and Biology 131: 103249. PubMed PMC

Mitchell AL, Attwood TK, Babbitt PC, PubMed PMC

Mosseray R. (1934). Les

Nargesi S, Jafarzadeh J, Najafzadeh MJ, PubMed

Negri CE, Gonçalves SS, Xafranski H, PubMed PMC

Nguyen L-T, Schmidt HA, von Haeseler A, PubMed PMC

Nielsen KF, Mogensen JM, Johansen M, PubMed

Noonim P, Mahakarnchanakul W, Nielsen KF, PubMed

Pante E, Puillandre N, Viricel A, PubMed

Paradis E. (2010). pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419–420. PubMed

Parker E, Dornburg A, Struthers CD, PubMed

Perrone G, Stea G, Epifani F, PubMed

Peterson SW. (2000). Phylogenetic relationships in

Peterson SW. (2008). Phylogenetic analysis of PubMed

Pitt JI, Hocking AD. (2009).

R Core Team (2016). R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria.

Raper KB, Fennell DI. (1965). The genus

Rawlings ND, Barrett AJ, Thomas PD, PubMed PMC

Richards TA. (2011). Genome evolution: horizontal movements in the fungi. Current Biology 21: R166–R168. PubMed

Rokas A, Williams BL, King N, PubMed

Ronquist F, Teslenko M, van der Mark P, PubMed PMC

Salah H, Lackner M, Houbraken J, PubMed PMC

Samson RA, Houbraken J, Thrane U,

Samson RA, Houbraken J, Thrane U,

Samson RA, Houbraken JAMP, Kuijpers AFA,

Samson RA, Hubka V, Varga J,

Samson RA, Noonim P, Meijer M, PubMed PMC

Schuster E, Dunn-Coleman N, Frisvad J, PubMed

Seekles SJ, Punt M, Savelkoel N, PubMed PMC

Seo T-K. (2008). Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Molecular Biology and Evolution 25: 960–971. PubMed

Seppey M, Manni M, Zdobnov EM. (2019). BUSCO: assessing genome assembly and annotation completeness. Methods in Molecular Biology 1962: 227–245. PubMed

Shen W, Le S, Li Y, PubMed PMC

Silva da JJ, Iamanaka BT, Ferranti LS, PubMed PMC

Sklenář F, Glässnerová K, Jurjević Ž, PubMed PMC

Sklenář F, Jurjević Ž, Houbraken J, PubMed PMC

Sklenář F, Jurjević Ž, Zalar P, PubMed PMC

Slot JC, Rokas A. (2011). Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Current Biology 21: 134–139. PubMed

Stamatakis A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. PubMed PMC

Stanke M, Schöffmann O, Morgenstern B, PubMed PMC

Steenkamp ET, Wingfield MJ, McTaggart AR,

Steenwyk JL, Shen X-X, Lind AL, PubMed PMC

Steenwyk JL, Balamurugan C, Raja HA. PubMed DOI PMC

Sukumaran J, Holder MT, Knowles LL. (2021). Incorporating the speciation process into species delimitation. PLoS Computational Biology 17: e1008924. PubMed PMC

Swofford DL. (2003). PAUP* Phylogenetic analysis using parsimony, (*and other methods); version 4.0 b10. Sinauer Associates, USA.

Szigeti G, Sedaghati E, Mahmoudabadi AZ, PubMed

Szöllősi GJ, Davín AA, Tannier E, PubMed PMC

Talavera G, Castresana J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564–577. PubMed

Taniwaki MH, Pitt JI, Magan N. (2018).

Taylor JW, Jacobson DJ, Kroken S, PubMed

Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, PubMed PMC

Thom C. (1916).

Thom C, Church MB. (1926). The Aspergilli. Baltimore: Williams & Wilkins.

Thom C, Raper KB. (1945). A Manual of the Aspergilli. Baltimore: Williams & Wilkins.

Turland NJ, Wiersema JH, Barrie FR,

van Rossum G, Drake FL., Jr (2014). The python language reference. Python software foundation.

Varga J, Szigeti G, Baranyi N, PubMed

Varga J, Frisvad JC, Kocsubé S, PubMed PMC

Varga J, Kevei F, Vriesema A, PubMed

Vaser R, Sović I, Nagarajan N, PubMed PMC

Vesth TC, Nybo JL, Theobald S, PubMed

Vidal-Acuña MR, Ruiz M, Torres MJ, PubMed

Wang PM, Liu X bin, Dai YC,

Ward OP. (1989). Fermentation Biotechnology. Prentice Hall, Englewood Cliffs, New York, USA.

Wehmer C. (1907). Zur Kenntnis einiger

Wilhelm KA. (1877). Beiträge zur Kenntnis des Pilzgattung Aspergillus. Doctoral Dissertation, Strasburg, Germany.

Woudenberg JHC, Seidl MF, Groenewald JZ, PubMed PMC

Yamada O, Takara R, Hamada R, PubMed

Yang L, Lübeck M, Lübeck PS. (2017).

Yang Z. (2015). The BPP program for species tree estimation and species delimitation. Current Zoology 61: 854–865.

Yang Z, Rannala B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences 107: 9264–9269. PubMed PMC

Yang Z, Rannala B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution 31: 3125–3135. PubMed PMC

Yin Y, Mao X, Yang J, PubMed PMC

Yu T-S, Yeo S-H, Kim H-S. (2004). A new species of hyphomycetes,

Zerbino DR, Birney E. (2008). Velvet: algorithms for PubMed PMC

Aspergillus latus: A cryptic causative agent of aspergillosis emerging in Japan

Resolving Phylogenetic Relationships Within the Trichophyton mentagrophytes Complex: A RADseq Genomic Approach Challenges Status of 'Terbinafine-Resistant' Trichophyton indotineae as Distinct Species

A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

Defining the relationship between phylogeny, clinical manifestation, and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations

A monograph of Aspergillus section Candidi

Zobrazit více v PubMed

Dryad
10.5061/dryad.866t1g1td