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3. IMA Genome – F19: A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras

Author

Aylward, Janneke, Wilson, Andi M., Visagie, Cobus M., Spraker, Joseph, Barnes, Irene, Buitendag, Carla, Ceriani, Callin, Del Mar Angel, Lina, du Plessis, Deanné, Fuchs, Taygen, Gasser, Katharina, Krämer, Daniella, Li, WenWen, Munsamy, Kiara, Piso, Anja, Price, Jenna-Lee, Sonnekus, Byron, Thomas, Chanel, van der Nest, Ariska, van Dijk, Alida, van Heerden, Alishia, van Vuuren, Nicole, Yilmaz, Neriman, Duong, Tuan A., van der Merwe, Nicolaas A., Wingfield, Michael J., and Wingfield, Brenda D.

Published
2024
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5. IMA genome-F18

Author

Visagie, Cobus M, Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A, Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E, Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C, Hakalova, Eliska, Hayes, Richard D, Houbraken, Jos, Grigoriev, Igor V, LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J, Zhang, Yu, and Wingfield, Brenda D

Subjects
Microbiology, Plant Biology, Biological Sciences, Plant biology
Published
2023

8. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicilliumbiforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Published
2023
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9. Sporothrix and Sporotrichosis: A South African Perspective on a Growing Global Health Threat.

Author

Fuchs, Taygen, Visagie, Cobus M., Wingfield, Brenda D., and Wingfield, Michael J.

Subjects
*EMERGING infectious diseases, *MYCOSES, *SPOROTRICHOSIS, *GOLD mining, SOUTH African history
Abstract

Sporotrichosis is a disease that arises from a fungal infection caused by members of the Ascomycete genus Sporothrix. The disease has a unique history in South Africa, due to an association with gold mines, where large numbers of mine workers were infected in the 1930s and 1940s. This was likely driven by hot humid conditions and timber supports used in these mine shafts. Furthermore, the disease is the most common subcutaneous fungal infection amongst the general population in South Africa, and the large number of immunocompromised individuals increases the public health risk in the country. Sporothrix is a genus in the Ophiostomatales, a fungal order primarily associated with environmental habitats. Unsurprisingly, sporotrichosis therefore has a documented history of sapronotic transmission from contaminated plant material. This review provides insights into the understanding of sporotrichosis and Sporothrix species, with a particular emphasis on the South African situation. We highlight knowledge gaps, particularly regarding the ecological factors influencing the occurrence and distribution of these species, which in turn affect the patterns of sporotrichosis. We also emphasise a need for ongoing proactive research and surveillance to prevent future outbreaks of sporotrichosis, an emerging disease with growing health implications worldwide. [ABSTRACT FROM AUTHOR]

Published
2024
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11. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, Wingfield, Brenda D., Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Published
2023

12. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Ministry of Education, Youth and Sports (Czech Republic), Mendel University, Department of Energy (US), Joint Genome Institute (US), Bioenergy Research Center (US), Department of Science and Innovation (South Africa), National Research Foundation (South Africa), Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, Angelis, Maria de, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, Wingfield, Brenda D., Ministry of Education, Youth and Sports (Czech Republic), Mendel University, Department of Energy (US), Joint Genome Institute (US), Bioenergy Research Center (US), Department of Science and Innovation (South Africa), National Research Foundation (South Africa), Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, Angelis, Maria de, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Abstract

Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.

Published
2023

15. Fungi and their mycotoxins associated with maize ear rots from emerging maize farms in the Eastern Cape, South Africa

Author

Jenna-Lee Price, Yilmaz, Neriman, and Visagie, Cobus M.

Subjects
Ear rot, maize, multiple mycotoxins
Abstract

Maize is South Africa’s most important crop. The Eastern Cape (EC) has been identified as an area of strategic importance for increased production, however, research on diseases affecting production in the province is lacking. This baseline study thus surveyed for ear rots at EC farms and determined the species and mycotoxins present. Diseased maize ears were collected from 11 farms. Fungal isolations were made and strains identified using morphology and DNA sequence comparisons. Translation elongation factor 1- α was sequenced to identify Cladosporium, Fusarium and Stenocarpella strains. LC-MS/MS was used to test for the presence 14 mycotoxins, including aflatoxin B1, aflatoxin B2, aflatoxin G1, deoxynivalenol (DON), diplodiatoxin, 15-acetyl-deoxynivalenol (15-ADON), fumonisin B1 (FUM B1), fumonisin B2 (FUM B2), fumonisin B3 (FUM B3), HT-2, T2 and zearalenone (ZEA).Ninety-three fungal strains were isolated and found to belong to Fusarium (73%), Stenocarpella (19%) and Cladosporium (8%). Mycotoxigenic species detected included Fusarium boothii (DON), F. graminearum (DON and ZEA), F. oxysporum and F. verticillioides(FUM); F. poae, F. subglutinans and F. temperatum (various emerging mycotoxins); and Stenocarpella maydis (diplodiatoxin). Mycotoxin analysis indicated samples were contaminated with DON (58%), diplodiatoxin (58%), 15-ADON (42%) and ZEA (25%).This study found known mycotoxin producers and their associated mycotoxins. Mycotoxins were detected at elevated levels, with 45% of the samples found to be contaminated with multiple mycotoxins. The identification and preservation of the causal agents will allow future work to focus on understanding abiotic and biotic factors that influence mycotoxin production.&nbsp

Published
2022
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16. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov

Author

Visagie, Cobus M, Boekhout, Teun, Theelen, Bart, Dijksterhuis, Jan, Yilmaz, Neriman, Seifert, Keith A, Visagie, Cobus M, Boekhout, Teun, Theelen, Bart, Dijksterhuis, Jan, Yilmaz, Neriman, and Seifert, Keith A

Abstract

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.

Published
2022

17. Fungal Planet description sheets : 1436 –1477

Author

Tan, Yu Pei, Bishop-Hurley, Sharon L., Shivas, Roger G., Cowan, Don, Maggs-Kölling, Gillian, Maharachchikumbura, Sajeewa S. N., Pinruan, Umpawa, Bransgrove, Kaylene L., De la Peña-Lastra, Saúl, Larsson, Ellen, Lebel, Teresa, Mahadevakumar, Shivannegowda, Mateos, Antonio, Osieck, Eduard R., Rigueiro-Rodríguez, Antonio, Sommai, Sujinda, Ajithkumar, Kadaiah, Akulov, Alex, Anderson, Freda E., Arenas, Francisco, Balashov, Sergey, Bañares, Ángel, Berger, Dave K., Bianchinotti, María V., Bien, Steffen, Bilański, Piotr, Boxshall, Amelia-Grace, Bradshaw, Michael, Broadbridge, Jasmin, Calaça, Francisco J.S., Campos-Quiroz, Carolina, Carrasco-Fernández, Jorge, Castro, Jean F., Chaimongkol, Soravit, Chandranayaka, Siddaiah, Chen, Yanpeng, Comben, David, Dearnaley, John, Ferreira-Sá, Antônio S., Dhileepan, Kunjithapatham, Díaz, Marina L., Divakar, Pradeep K., Xavier-Santos, Solange, Fernández-Bravo, Ana, Gené, Josepa, Guard, Frances E., Guerra, Matías, Gunaseelan, Sugantha, Houbraken, Jos, Janik-Superson, Katarzyna, Jankowiak, Robert, Jeppson, Mikael, Jurjević, Želko, Kaliyaperumal, Malarvizhi, Kelly, Lisa A., Kezo, Kezhocuyi, Khalid, Abdul N., Khamsuntorn, Phongsawat, Kidanemariam, Dawit, Kiran, Munaza, Lacey, Ernest, Langer, Gitta J., López-Llorca, Luis V., Luangsa-ard, Janet J., Lueangjaroenkit, Piyangkun, Lumbsch, H. Thorsten, Maciá-Vicente, Jose G., Mamatha Bhanu, Lakkur S., Marney, Thomas S., Marqués-Gálvez, José E., Morte, Asunción, Naseer, Arooj, Navarro-Ródenas, Alfonso, Oyedele, Oluwawapelumi, Peters, Sandra, Piskorski, Sebastian, Quijada, Luis, Ramírez, Gustavo H., Raja, Kanaga valli, Razzaq, Annum, Rico, Víctor J., Rodríguez, Antonio, Ruszkiewicz-Michalska, Małgorzata, Sánchez, Romina M., Santelices, Cecilia, Savitha, Attihalli S., Serrano, Miguel, Leonardo-Silva, Lucas, Solheim, Halvor, Somrithipol, Sayanh, Sreenivasa, Marikunte Y., Stępniewska, Hanna, Strapagiel, Dominik, Taylor, Tamara, Torres-Garcia, Daniel, Vauras, Jukka, Villarreal, Manuel, Visagie, Cobus M., Wołkowycki, Marek, Yingkunchao, Wittayothin, Zapora, Ewa, Groenewald, Johannes Z., Crous, Pedro W., Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Microbial Ecology (ME), Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante. Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', and Fitopatología

Subjects
ITS nrDNA barcodes, LSU, new taxa, systematics, Plantenecologie en Natuurbeheer, Plant Ecology and Nature Conservation, Ecology, Evolution, Behavior and Systematics
Abstract

Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilax glyciphylla. Brazil, Preussia bezerrensis fromair. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola onsoilinmixedforest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.)and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareussoils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes.

Published
2022

18. Along the footpath of Penicillium discovery: Six new species from the Woodville Big Tree Forest Trail.

Author

Visagie, Cobus M. and Yilmaz, Neriman

Subjects
*RNA polymerase II, *PENICILLIUM, *OCHRATOXINS, *RIBOSOMAL DNA, *SPECIES, *TRAILS, *GENETIC barcoding
Abstract

In this study, we studied the diversity of Penicillium occurring in soil collected along the Woodville Big Tree Forest Trail situated close to the coastal town of Wilderness in South Africa. Strains were accessioned into a collection and then identified to species based on β-tubulin DNA sequences, which is the recommended DNA barcode for the genus. The 74 strains were found to represent 18 species, including six we consider undescribed. Here, we introduce them as Penicillium claroviride, P. kalander, P. mattheeae, P. outeniquaense, P. subfuscum, and P. umkhoba. Phylogenetic comparisons were made, and genealogical concordance was demonstrated for these new species using DNA sequences from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), β-tubulin, calmodulin, and RNA polymerase II second largest subunit. Notes on morphological characters distinguishing the new species from their close relatives are provided. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov.

Author

Visagie, Cobus M., Boekhout, Teun, Theelen, Bart, Dijksterhuis, Jan, Yilmaz, Neriman, and Seifert, Keith A.

Abstract

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture‐dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self‐portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H‐24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade‐old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi. Take‐away: Blastobotrys davincii is introduced as a new species.Surveys have detected this species, but could never correctly identify or name it.The species was found on the da Vinci portrait, mummies and other substrates.A nomenclature review and an accepted species list for the Blastobotrys/Trichomonascus clade is provided.Appropriate isolation media are important to allow for growth of specific fungi. [ABSTRACT FROM AUTHOR]

Published
2023
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21. Along the footpath of Penicilliumdiscovery: Six new species from the Woodville Big Tree Forest Trail

Author

Visagie, Cobus M. and Yilmaz, Neriman

Abstract

ABSTRACTIn this study, we studied the diversity of Penicilliumoccurring in soil collected along the Woodville Big Tree Forest Trail situated close to the coastal town of Wilderness in South Africa. Strains were accessioned into a collection and then identified to species based on β-tubulin DNA sequences, which is the recommended DNA barcode for the genus. The 74 strains were found to represent 18 species, including six we consider undescribed. Here, we introduce them as Penicillium claroviride, P. kalander, P. mattheeae, P. outeniquaense, P. subfuscum, and P. umkhoba. Phylogenetic comparisons were made, and genealogical concordance was demonstrated for these new species using DNA sequences from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), β-tubulin, calmodulin, and RNA polymerase II second largest subunit. Notes on morphological characters distinguishing the new species from their close relatives are provided.

Published
2023
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22. IMA Genome – F19

Author

Aylward, Janneke, Wilson, Andi M., Visagie, Cobus M., Spraker, Joseph, Barnes, Irene, Buitendag, Carla, Ceriani, Callin, Del Mar Angel, Lina, du Plessis, Deanné, Fuchs, Taygen, Gasser, Katharina, Krämer, Daniella, Li, WenWen, Munsamy, Kiara, Piso, Anja, Price, Jenna-Lee, Sonnekus, Byron, Thomas, Chanel, van der Nest, Ariska, van Dijk, Alida, van Heerden, Alishia, van Vuuren, Nicole, Yilmaz, Neriman, Duong, Tuan A., van der Merwe, Nicolaas A., Wingfield, Michael J., and Wingfield, Brenda D.

Abstract

The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. In this issue, we report on a Genome Assembly Workshop for Mycologists that was held at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa and make available the 12 draft genome sequences emanating from the event. With the aim of making the process of genome assembly and annotation more accessible to biologists, we provide a step-by-step guide to both genome assembly and annotation, intended to encourage and empower mycologists to use genome data in their research.

Published
2024
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23. New Resinogaleaspecies from Araucaria araucanaresin in Chile and reclassification of the genus in the Cryptocaliciomycetidae

Author

Balocchi, Felipe, Barnes, Irene, Wingfield, Michael J., Ahumada, Rodrigo, and Visagie, Cobus M.

Abstract

Araucaria araucanais an ancient conifer, native to the mountain ranges in Chile and Argentina. These trees host a large number of organisms, mainly insects, strongly or even exclusively associated with them. The recent emergence of a novel canker disease on A. araucanahas emphasised the importance of fungi associated with these iconic trees and has resulted in the discovery of various new species. In this study, we considered the identity of an unknown calicioid fungus consistently found on resin on the branches of A. araucana. Preliminary phylogenetic analyses placed isolates in the recently described sub-class Cryptocaliciomycetidae, closest to Cryptocalicium blascoi. However, the morphology of the ascomata and its occurrence in a unique niche suggested that the closest relative could be Resinogalea humboldtensis(Bruceomycetaceae, incertae sedis), a fungus with similar sporing structures found on resin of Araucaria humboldtensisin New Caledonia. There are no living cultures or sequence data available for either R. humboldtensisor its supposed closest relative, Bruceomyces castoris,precluding sequence-based comparisons. Morphological comparisons of the sporing structures on A. araucanaconfirmed that the ascomatal morphology of our unknown calicioid fungus and R. humboldtensisare almost identical and resemble each other more so than B. castorisor Cr. blascoi. A phylogenetic analysis based on the small subunit (SSU), internal transcribed spacer (ITS) and large subunit (LSU) rDNA regions resolved our strains into two clades with Cr. blascoias its closest relative. Further analyses applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) based on ITS, mini chromosome maintenance protein complex (MCM7), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF) gene regions, confirmed that strains represent two new species. Based on our morphological observations and phylogenetic analyses, we introduce two new Resinogaleaspecies, R. araucanaand R. tapulicola,and reclassify the genus in the subclass Cryptocaliciomycetidae.

Published
2023
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