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Song WL, Li M, Wang ZQ, Chen SL. Taxonomy and phylogeny of three species in Perichaena sensu lato (Myxomycetes = Myxogastria) from China. Eur J Protistol 2024; 95:126105. [PMID: 38908307 DOI: 10.1016/j.ejop.2024.126105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
After Gulielmina was erected and Ophiotheca was resurrected based on some species originally included in Perichaena (Trichiaceae, Trichiales, Myxomyxetes), some specimens from the Herbarium of Fungi of Nanjing Normal University previously identified as Perichaena species were reexamined from morphological and two-gene (nuclear 18S rDNA and elongation factor-1 alpha) phylogenetic perspectives. In this study, two new myxomycete species, Gulielmina subreticulospora and Ophiotheca dictyospora, are described. Gulielmina subreticulospora shows the following character combination: branched plasmodiocarps, single peridium with circular protrusions in the inner surface, capillitium (2.4-)2.8-3.0(-3.4) μm in diameter, spores (7.4-)8.0-8.5(-9.0) μm in diameter and sub-reticulated. Ophiotheca dictyospora shows the following character combination: sessile sporocarps to short plasmodiocarps, single peridium with a densely irregular network and protrusions in the inner surface, capillitium (2.7-)3.5-5.0(-7.1) μm in diameter, uneven, decorated with spines of uneven size, spores (7.7-)8.2-8.6(-9.4) μm in diameter including obviously complete cristate reticulation with serrated edges, with deep and clear grids. Both new taxa were compared with related species and their genetic isolation was statistically tested. Moreover, a comprehensive morphological description and a detailed figure plate are provided for Perichaena verrucifera, and its phylogenetic position is determined.
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Min Li
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, Shandong Province, China
| | - Zi-Qi Wang
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China.
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Song WL, Yan SZ, Chen SL. Morphological and phylogenetic analyses reveal four species of myxomycetes new to China. Arch Microbiol 2024; 206:364. [PMID: 39080072 DOI: 10.1007/s00203-024-04083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 08/15/2024]
Abstract
Four species of myxomycetes (Arcyria pseudodenudata, Diderma europaeum, Lycogala irregulare, and Trichia armillata) new to China were observed via light microscope and scanning electron microscope, and detailed descriptions and illustrations are provided, along with comparisons with related species. Among them, A. pseudodenudata was discovered for the first time outside of the type locality, D. europaeum was discovered for the first time outside of Europe, and L. irregulare and T. armillata were reported again after being named. Phylogenetic analyses based on nuclear 18S rDNA and elongation factor-1 alpha sequences or nuclear 18S rDNA and cytochrome oxidase subunit I sequences was performed to provide a molecular basis for morphological identification. These specimens were deposited in the Herbarium of Fungi of Nanjing Normal University.
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China.
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3
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Song WL, Chen SL. Arcyria similaris: A new myxomycete species from China. Mycologia 2024; 116:409-417. [PMID: 38442243 DOI: 10.1080/00275514.2024.2312077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024]
Abstract
A new myxomycete species, Arcyria similaris, was reported herein. The specimens were found and collected in the field on dead bark from Jingangtai National Geopark in Henan Province of China. This species has distinct and unique morphological characteristics, including dark grayish olive sporothecae that fade to smoke gray with age, shallow saucer-shaped cups with marked reticulations and thick papillae on the inner surface, a netted capillitium with many bulges, uniformly marked with low, dense, and irregular reticulations, and spores (8.0-)9.3-10.1(-10.9) μm in diameter, marked with sparse small warts and grouped prominent warts. Apart from a comprehensive morphological study, partial sequences of the nuclear 18S rDNA and elongation factor-1 alpha (EF-1α) genes were also provided in this study. This new species was described and illustrated morphologically. The specimens are deposited in the Herbarium of Fungi of Nanjing Normal University (HFNNU).
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
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4
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Shchepin ON, López Villalba Á, Inoue M, Prikhodko IS, Erastova DA, Okun MV, Woyzichovski J, Yajima Y, Gmoshinskiy VI, Moreno G, Novozhilov YK, Schnittler M. DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia. Protist 2024; 175:126023. [PMID: 38368650 DOI: 10.1016/j.protis.2024.126023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.
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Affiliation(s)
- Oleg N Shchepin
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany; Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia.
| | - Ángela López Villalba
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Maho Inoue
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Ilya S Prikhodko
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Daria A Erastova
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Mikhail V Okun
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Jan Woyzichovski
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Yuka Yajima
- Department of Science and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, 0508585 Muroran, Japan
| | - Vladimir I Gmoshinskiy
- Department of Mycology and Algology, Faculty of Biology, Moscow State University, Leninskie Gory 1/12, Moscow 119992, Russia
| | - Gabriel Moreno
- Departamento Ciencias de la Vida (Botanica), Universidad de Alcala, Alcala de Henares, Madrid 28805, Spain
| | - Yuri K Novozhilov
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
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Wei S, Li S, Liu P, Qi B, Wang Q, Li Y. Didymium arenosum, a myxomycete new to science from the confluence of deserts in northwestern China. PeerJ 2024; 12:e16725. [PMID: 38213774 PMCID: PMC10782953 DOI: 10.7717/peerj.16725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
A new myxomycete species, Didymium arenosum, was described based on morphological evidence and phylogenetic analyses. The species was discovered in the arid region at the confluence of the Badain Jaran desert and Tengger desert on the leaves of Betula platyphylla and was cultivated in a moist chamber culture. Morphologically, the species is distinguished by the greenish-yellow calcium carbonate crystals on the surface and the spores covered with small warts, some of which are connected into a short line. A phylogenetic analysis of D. arenosum strongly supports its classification as a separate clade. The spore to spore agar culture of D. arenosum requires 23 days, and this study provides a detailed description of its life cycle.
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Affiliation(s)
- Shuwei Wei
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
- Northeast Normal University, Changchun, Jilin, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
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García-Martín J, Zamora J, Lado C. Multigene phylogeny of the order Physarales ( Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. PERSOONIA 2023; 51:89-124. [PMID: 38665983 PMCID: PMC11041899 DOI: 10.3767/persoonia.2023.51.02] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/04/2022] [Indexed: 04/28/2024]
Abstract
The class Myxomycetes consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order Physarales, with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, EF-1α, α-Tub, and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family Didymiaceae is paraphyletic to the rest of Physarales. Within Didymiaceae s.lat., the recent reinstatement of the genus Polyschismium for most species traditionally ascribed to Lepidoderma, except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus Mucilago in Didymium and Lepidoderma s.str. (L. tigrinum) in Diderma (Prikhodko et al. 2023). Additionally, the genus Diachea is redefined to include some species previously treated in Physaraceae (Craterium spp. with true columella). Within the monophyletic family Physaraceae, most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within Physaraceae prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, Nannengaella, is proposed for a major clade containing Physarum globuliferum and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) Lignydium is resurrected for the clade containing Fuligo muscorum. Additionally, Trichamphora is suggested as the correct name for the clade containing Physarum pezizoideum. The taxonomy and nomenclature of some provisional genera, currently synonymous with Fuligo and Physarum, are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided. Citation: García-Martín JM, Zamora JC, Lado C. 2023. Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. Persoonia 51: 89-124. doi: 10.3767/persoonia.2023.51.02.
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Affiliation(s)
- J.M. García-Martín
- Department of Mycology, Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
- Conservatoire et Jardin botaniques de la Ville de Genève, Chem. de l’Impératrice 1, 1292 Pregny-Chambésy, Switzerland
| | - C. Lado
- Department of Mycology, Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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7
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A three-gene phylogeny supports taxonomic rearrangements in the family Didymiaceae (Myxomycetes). Mycol Prog 2023. [DOI: 10.1007/s11557-022-01858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Lado C, Treviño-Zevallos I, García-Martín JM, Wrigley de Basanta D. Diachea mitchellii: A new myxomycete species from high elevation forests in the tropical Andes of Peru. Mycologia 2022; 114:798-811. [PMID: 35695815 DOI: 10.1080/00275514.2022.2072140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new species of the genus Diachea (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and phylogenetic data, are provided. At first glance, the new species shares some morphological similarities with both D. leucopodia, type of the genus, and D. koazei, but it strikingly differs from all other species of its genus by combining a short dark stalk, with a reticulate columella, and clustered spores. Moreover, it seems to be the only species of Diachea exclusively associated with Polylepis tropical forests at elevations above 3500 m. Apart from a comprehensive morphological study of 31 specimens, we here provide phylogenetic evidence to confirm the inclusion of this species in the genus Diachea. Specifically, our phylogenetic analyses of the nuclear 18S rDNA (18S), mitochondrial 17S rDNA (17S), and elongation factor-1 alpha (EF-1α) genes show that the new species is related to D. leucopodia and D. bulbillosa. The remarkably different morphological characters distinguishing the new Diachea from all other species of its genus, along with its particular ecological preferences and geographic distribution, indicate that it is a distinct entity deserving recognition as an independent species.
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Affiliation(s)
- Carlos Lado
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
| | | | - Joaquina María García-Martín
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
| | - Diana Wrigley de Basanta
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
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Ronikier A, García-Cunchillos I, Janik P, Lado C. Nivicolous Trichiales from the austral Andes: unexpected diversity including two new species. Mycologia 2020; 112:753-780. [PMID: 32649270 DOI: 10.1080/00275514.2020.1759978] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Nivicolous myxomycetes are a group of amoebozoan protists dependent on long-lasting snow cover worldwide. Recent fine-scale analysis of species diversity from the austral Andes revealed high intraspecific variability of most taxa, suggesting independent evolutionary processes and significant differences in species compositions between the Northern (NH) and Southern (SH) Hemispheres. The present study is the second part of this analysis based on representatives of Trichiales. A total of 173 South American collections were studied based on morphological and molecular data, and 15 taxa have been identified. Two of them, Hemitrichia crassifila and Perichaena patagonica, are proposed as new species confirmed by a phylogeny of Trichiales. However, their affinity to the genera in which they are proposed are not confirmed due to polyphyletic character of all genera of Trichiales. Four species, Dianema subretisporum, Trichia contorta var. karstenii, T. nivicola, and T. sordida, are reported for the first time from the Southern Hemisphere. One species, T. alpina, is new for Argentina. Additionally, we provide the first record of Perichaena megaspora from Chile. Specimen frequency and species diversity of Trichiales found at nivicolous localities in the austral Andes are unexpectedly high, exceeding those of Stemonitidales, the most numerous group in the Northern Hemisphere, where Trichiales play a marginal role. By contrast, Trichiales appear the main component of nivicolous assemblages in the Andes. Results of the present work, together with the earlier analysis of Stemonitidales, indicate that the Andes constitute an exceptionally important evolutionary hot spot for nivicolous myxomycetes characterized by an outstanding species diversity.
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Affiliation(s)
- Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences , Lubicz 46, 31-512 Kraków, Poland
| | - Iván García-Cunchillos
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas , Plaza de Murillo 2, 28014 Madrid, Spain
| | - Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences , Lubicz 46, 31-512 Kraków, Poland
| | - Carlos Lado
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas , Plaza de Murillo 2, 28014 Madrid, Spain
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Janik P, Ronikier M, Ronikier A. New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes. PeerJ 2020; 8:e8406. [PMID: 32002333 PMCID: PMC6984339 DOI: 10.7717/peerj.8406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/16/2019] [Indexed: 11/23/2022] Open
Abstract
Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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