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Minio A, Figueroa-Balderas R, Cohen SP, Ali SS, Carriel D, Britto D, Stack C, Baruah IK, Marelli JP, Cantu D, Bailey BA. Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion. G3 (BETHESDA, MD.) 2023; 13:jkad125. [PMID: 37337677 PMCID: PMC10468315 DOI: 10.1093/g3journal/jkad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
- Genome Center, University of California Davis, 95616 Davis, CA, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Stephen P Cohen
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Denny Carriel
- Mars La Chola (MLCH), Mars Inc., Guayaquil 090103, Ecuador
| | - Dahyana Britto
- Mars Center for Cocoa Science, Mars Inc., Fazenda Almirante, Caixa Postal 55, Itajuípe, BA, CEP 45630-000, Brazil
| | - Conrad Stack
- Mars Digital Technologies, Mars Inc., Chicago 60642, IL, USA
| | - Indrani K Baruah
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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Ramírez-Camejo LA, Eamvijarn A, Díaz-Valderrama JR, Karlsen-Ayala E, Koch RA, Johnson E, Pruvot-Woehl S, Mejía LC, Montagnon C, Maldonado-Fuentes C, Aime MC. Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range. PHYTOPATHOLOGY 2022; 112:643-652. [PMID: 34428920 DOI: 10.1094/phyto-06-21-0255-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.
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Affiliation(s)
- Luis A Ramírez-Camejo
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
- Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton, Panama, Republic of Panama
| | - Amnat Eamvijarn
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Department of Agriculture, Chatuchak, Bangkok, Thailand
| | - Jorge R Díaz-Valderrama
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elena Karlsen-Ayala
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- University of Florida, Department of Plant Pathology, Gainesville, FL, U.S.A
| | - Rachel A Koch
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elizabeth Johnson
- Inter-American Institute for Cooperation on Agriculture, Hope Gardens, Kingston, Jamaica
| | | | - Luis C Mejía
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
| | | | | | - M Catherine Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
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Coffee Leaf Rust (Hemileia vastatrix) from the Recent Invasion into Hawaii Shares a Genotypic Relationship with Latin American Populations. J Fungi (Basel) 2022; 8:jof8020189. [PMID: 35205944 PMCID: PMC8877902 DOI: 10.3390/jof8020189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/10/2022] Open
Abstract
Hawaii has long been one of the last coffee-producing regions of the world free of coffee leaf rust (CLR) disease, which is caused by the biotrophic fungus Hemileia vastatrix. However, CLR was detected in coffee farms and feral coffee on the island of Maui in February 2020 and subsequently on other islands of the Hawaiian archipelago. The source of the outbreak in Hawaii is not known, and CLR could have entered Hawaii from more than 50 coffee-producing nations that harbor the pathogen. To determine the source(s) of the Hawaii inoculum, we analyzed a set of eleven simple sequence repeat markers (SSRs) generated from Hawaii isolates within a dataset of 434 CLR isolates collected from 17 countries spanning both old and new world populations, and then conducted a minimum spanning network (MSN) analysis to trace the most likely pathway that H. vastatrix could have taken to Hawaii. Forty-two multilocus genotypes (MLGs) of H. vastatrix were found in the global dataset, with all isolates from Hawaii assignable to MLG 10 or derived from it. MLG 10 is widespread in Central America and Jamaica, making this region the most probable source of inoculum for the outbreak in Hawaii. An examination of global weather patterns during the months preceding the introduction of CLR makes it unlikely that the pathogen was windborne to the islands. Likely scenarios for the introduction of CLR to Hawaii are the accidental introduction of spores or infected plant material by travelers or seasonal workers, or improperly fumigated coffee shipments originating from Central America or the Caribbean islands.
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Ali SS, Amoako-Attah I, Shao J, Kumi-Asare E, Meinhardt LW, Bailey BA. Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae. Front Microbiol 2021; 12:752094. [PMID: 34777305 PMCID: PMC8581569 DOI: 10.3389/fmicb.2021.752094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/01/2021] [Indexed: 11/23/2022] Open
Abstract
Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Jonathan Shao
- U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville, MD, United States
| | | | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
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6
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Jiang JH, Wu SH, Zhou LW. The First Whole Genome Sequencing of Sanghuangporus sanghuang Provides Insights into Its Medicinal Application and Evolution. J Fungi (Basel) 2021; 7:jof7100787. [PMID: 34682209 PMCID: PMC8537844 DOI: 10.3390/jof7100787] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 01/06/2023] Open
Abstract
Sanghuangporus is a medicinal macrofungal genus typified by S. sanghuang, the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of S. sanghuang, we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33.34 Mb genome sequence was assembled to 26 contigs, which lead to the prediction of 8278 protein-coding genes. From these genes, the potential biosynthesis pathway of sesquiterpenoids was, for the first time, identified from Sanghuangporus, besides that of triterpenoids. While polysaccharides are the main medicinal metabolites in S. sanghuang, flavonoids are especially abundant medicinal metabolites comparing with other medicinal macrofungal groups. From the genomic perspective, S. sanghuang has a tetrapolar heterothallic mating system, and has its special nutritional strategy and advantageous medicinal properties compared with S. baumii and S. vaninii. A phylogenomics analysis indicates that Sanghuangporus emerged 15.39 million years ago and S. sanghuang has a closer phylogenetic relationship with S. baumii than S. vaninii. However, S. sanghuang shares a higher region of synteny and more orthologous genes, including carbohydrate-active enzymes with S. vaninii than S. baumii. A comparative genomics analysis with S. baumii and S. vaninii indicates that species diversification within Sanghuangporus may be driven by the translocation and translocation plus inversion of genome sequences, while the expansion and contraction of gene families may contribute to the host specificity of Sanghuangporus species. In general, the genome sequence of S. sanghuang provides insights into its medicinal application and evolution.
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Affiliation(s)
- Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Sheng-Hua Wu
- Department of Biology, National Museum of Natural Science, Taichung 404, China;
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence:
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Abstract
Sexual reproduction in fungi relies on proteins with well-known functions encoded by the mating type (MAT) loci. In the Basidiomycota, MAT loci are often bipartite, with the P/R locus encoding pheromone precursors and pheromone receptors and the HD locus encoding heterodimerizing homeodomain transcription factors (Hd1/Hd2). The interplay between different alleles of these genes within a single species usually generates at least two compatible mating types. However, a minority of species are homothallic, reproducing sexually without an obligate need for a compatible partner. Here, we examine the organization and function of the MAT loci of Cystofilobasidium capitatum, a species in the order Cystofilobasidiales, which is unusually rich in homothallic species. We determined MAT gene content and organization in C. capitatum and found that it resembles a mating type of the closely related heterothallic species Cystofilobasidium ferigula To explain the homothallic sexual reproduction observed in C. capitatum, we examined HD protein interactions in the two Cystofilobasidium species and determined C. capitatum MAT gene expression both in a natural setting and upon heterologous expression in Phaffia rhodozyma, a homothallic species belonging to a clade sister to that of Cystofilobasidium. We conclude that the molecular basis for homothallism in C. capitatum appears to be distinct from that previously established for P. rhodozyma Unlike in the latter species, homothallism in C. capitatum may involve constitutive activation or dispensability of the pheromone receptor and the functional replacement of the usual Hd1/Hd2 heterodimer by an Hd2 homodimer. Overall, our results suggest that homothallism evolved multiple times within the Cystofilobasidiales.IMPORTANCE Sexual reproduction is important for the biology of eukaryotes because it strongly impacts the dynamics of genetic variation. In fungi, although sexual reproduction is usually associated with the fusion between cells belonging to different individuals (heterothallism), sometimes a single individual is capable of completing the sexual cycle alone (homothallism). Homothallic species are unusually common in a fungal lineage named Cystofilobasidiales. Here, we studied the genetic bases of homothallism in one species in this lineage, Cystofilobasidium capitatum, and found it to be different in several aspects from those of another homothallic species, Phaffia rhodozyma, belonging to the genus most closely related to Cystofilobasidium Our results strongly suggest that homothallism evolved independently in Phaffia and Cystofilobasidium, lending support to the idea that transitions between heterothallism and homothallism are not as infrequent as previously thought. Our work also helps to establish the Cystofilobasidiales as a model lineage in which to study these transitions.
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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9
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Niveiro N, Ramírez NA, Michlig A, Lodge DJ, Aime MC. Studies of Neotropical tree pathogens in Moniliophthora: a new species, M. mayarum, and new combinations for Crinipellis ticoi and C. brasiliensis. MycoKeys 2020; 66:39-54. [PMID: 32273793 PMCID: PMC7136302 DOI: 10.3897/mycokeys.66.48711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 11/15/2022] Open
Abstract
The crinipelloid genera Crinipellis and Moniliophthora (Agaricales, Marasmiaceae) are characterized by basidiomes that produce long, dextrinoid, hair-like elements on the pileus surface. Historically, most species are believed to be saprotrophic or, rarely, parasitic on plant hosts. The primary morphological diagnostic characters that separate Crinipellis and Moniliophthora are pliant vs. stiff (Crinipellis) stipes and a tendency toward production of reddish pigments (ranging from violet to orange) in the basidiome in Moniliophthora. Additionally, most species of Moniliophthora appear to have a biotrophic habit, while those of Crinipellis are predominantly saprotrophic. Recently, several new neotropical collections prompted a morphological and phylogenetic analysis of this group. Herein, we propose a new species and two new combinations: Moniliophthoramayarumsp. nov., described from Belize, is characterized by its larger pileus and narrower basidiospores relative to other related species; Moniliophthoraticoicomb. nov. (= Crinipellisticoi) is recollected and redescribed from biotrophic collections from northern Argentina; and M.brasiliensiscomb. nov. (= Crinipellisbrasiliensis), a parasite of Heteropterysacutifolia. The addition of these three parasitic species into Moniliophthora support a hypothesis of a primarily biotrophic/parasitic habit within this genus.
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Affiliation(s)
- Nicolás Niveiro
- Instituto de Botánica del Nordeste (IBONE), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Sargento Cabral 2131, CC 209 Corrientes Capital, CP 3400, Argentina Consejo Nacional de Investigaciones Científicas y Tecnológicas Corrientes Argentina.,Departamento de Biología, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste. Av. Libertad 5470, Corrientes Capital, CP 3400, Argentina Universidad Nacional del Nordeste Corrientes Argentina
| | - Natalia A Ramírez
- Instituto de Botánica del Nordeste (IBONE), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Sargento Cabral 2131, CC 209 Corrientes Capital, CP 3400, Argentina Consejo Nacional de Investigaciones Científicas y Tecnológicas Corrientes Argentina.,Departamento de Biología, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste. Av. Libertad 5470, Corrientes Capital, CP 3400, Argentina Universidad Nacional del Nordeste Corrientes Argentina
| | - Andrea Michlig
- Instituto de Botánica del Nordeste (IBONE), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET). Sargento Cabral 2131, CC 209 Corrientes Capital, CP 3400, Argentina Consejo Nacional de Investigaciones Científicas y Tecnológicas Corrientes Argentina.,Departamento de Biología, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste. Av. Libertad 5470, Corrientes Capital, CP 3400, Argentina Universidad Nacional del Nordeste Corrientes Argentina
| | - D Jean Lodge
- Department of Plant Pathology, University of Georgia, Athens, GA 30606, USA University of Georgia Athens United States of America
| | - M Catherine Aime
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, 47907-2054, USA Purdue University West Lafayette United States of America
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10
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Marelli JP, Guest DI, Bailey BA, Evans HC, Brown JK, Junaid M, Barreto RW, Lisboa DO, Puig AS. Chocolate Under Threat from Old and New Cacao Diseases. PHYTOPATHOLOGY 2019; 109:1331-1343. [PMID: 31115251 DOI: 10.1094/phyto-12-18-0477-rvw] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Theobroma cacao, the source of chocolate, is affected by destructive diseases wherever it is grown. Some diseases are endemic; however, as cacao was disseminated from the Amazon rain forest to new cultivation sites it encountered new pathogens. Two well-established diseases cause the greatest losses: black pod rot, caused by several species of Phytophthora, and witches' broom of cacao, caused by Moniliophthora perniciosa. Phytophthora megakarya causes the severest damage in the main cacao producing countries in West Africa, while P. palmivora causes significant losses globally. M. perniciosa is related to a sister basidiomycete species, M. roreri which causes frosty pod rot. These Moniliophthora species only occur in South and Central America, where they have significantly limited production since the beginnings of cacao cultivation. The basidiomycete Ceratobasidium theobromae causing vascular-streak dieback occurs only in South-East Asia and remains poorly understood. Cacao swollen shoot disease caused by Cacao swollen shoot virus is rapidly spreading in West Africa. This review presents contemporary research on the biology, taxonomy and genomics of what are often new-encounter pathogens, as well as the management of the diseases they cause.
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Affiliation(s)
| | - David I Guest
- 2Sydney Institute of Agriculture, School of Life and Environmental Sciences, the University of Sydney, NSW 2006, Australia
| | - Bryan A Bailey
- 3USDA-ARS/Sustainable Perennial Crops Lab, Beltsville, MD 20705, U.S.A
| | | | - Judith K Brown
- 5School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, U.S.A
| | - Muhammad Junaid
- 2Sydney Institute of Agriculture, School of Life and Environmental Sciences, the University of Sydney, NSW 2006, Australia
- 8Cocoa Research Group/Faculty of Agriculture, Hasanuddin University, 90245 Makassar, Indonesia
| | | | | | - Alina S Puig
- 7USDA-ARS/Subtropical Horticultural Research Station, Miami, FL 33131, U.S.A
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11
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Bailey BA, Evans HC, Phillips‐Mora W, Ali SS, Meinhardt LW. Moniliophthora roreri, causal agent of cacao frosty pod rot. MOLECULAR PLANT PATHOLOGY 2018; 19:1580-1594. [PMID: 29194910 PMCID: PMC6638017 DOI: 10.1111/mpp.12648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Taxonomy: Moniliophthora roreri (Cif.) H.C. Evans et al. ; Phylum Basidiomycota; Class Agaricomycetes; Order Agaricales; Family Marasmiaceae; Genus Moniliophthora. Biology: Moniliophthora roreri attacks Theobroma and Herrania species causing frosty pod rot. Theobroma cacao (cacao) is the host of major economic concern. Moniliophthora roreri is a hemibiotroph with a long biotrophic phase (45-90 days). Spore masses, of apparent asexual origin, are produced on the pod surface after initiation of the necrotrophic phase. Spores are spread by wind, rain and human activity. Symptoms of the biotrophic phase can include necrotic flecks and, in some cases, pod malformation, but pods otherwise remain asymptomatic. Relationship to Moniliophthora perniciosa: Moniliophthora roreri and Moniliophthora perniciosa, causal agent of witches' broom disease of cacao, are closely related. Their genomes are similar, including many of the genes they carry which are considered to be important in the disease process. Moniliophthora perniciosa, also a hemibiotroph, has a typical basidiomycete lifestyle and morphology, forming clamp connections and producing mushrooms. Basidiospores infect meristematic tissues including flower cushions, stem tips and pods. Moniliophthora roreri does not form clamp connections or mushrooms and infects pods only. Both pathogens are limited to the Western Hemisphere and are a threat to cacao production around the world. Agronomic importance: Disease losses caused by frosty pod rot can reach 90% and result in field abandonment. Moniliophthora roreri remains in the invasive phase in the Western Hemisphere, not having reached Brazil, some islands within the Caribbean and a few specific regions within otherwise invaded countries. DISEASE MANAGEMENT The disease can be managed by a combination of cultural (for example, maintenance of tree height and removal of infected pods) and chemical methods. These methods benefit from regional application, but can be cost prohibitive. Breeding for disease resistance offers the greatest potential for frosty pod rot management and new tolerant materials are becoming available.
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Affiliation(s)
- Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | | | - Wilbert Phillips‐Mora
- Tropical Agricultural Research and Higher Education Center (CATIE)Turrialba 7170Costa Rica
| | - Shahin S. Ali
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
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12
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Bailey BA, Ali SS, Strem MD, Meinhardt LW. Morphological variants of Moniliophthora roreri on artificial media and the biotroph/necrotroph shift. Fungal Biol 2018; 122:701-716. [PMID: 29880205 DOI: 10.1016/j.funbio.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 11/24/2022]
Abstract
Moniliophthora roreri (Mr) causes frosty pod rot of Theobroma cacao in a hemibiotrophic association. The Mr biotroph-like phase has not been studied in culture. Mr spores (isolates Co12, Co52, and B3) were germinated on high (V8) and low (BPMM) nutrients with different media hardness (0.5% to 3% agarose). Germination was high on V8 media. Hardness affected germination on BPMM. Most colonies on V8 were slow-growing, failing to sporulate. Colony morphology depended on the isolate. On BPMM, exaggerated mycelia formed of limited length with enlarged cells. On agarose, rapidly expanding sporulating necrotrophic colonies formed rarely. Co12 and B3 spores were germinated on V8 and BPMM with low melting point (LMP) agarose. Slow-growing colonies of B3 on BPMM were unstable on LMP agarose, often forming slow-growing/rapidly expanding hybrids. Slow-growing colonies are hypothesized to represent the biotrophic phase. One nucleus was common in Mr cells, other than spores. Binucleate cells were occasionally observed in aged cells of slow-growing mycelia. Co52 cells often had more than two nuclei per cell after germination. Mr mycelia cells typically carry a single nucleus, being considered haploid. Biotroph- and necrotroph-like mycelia displayed differential gene expression but results were inconsistent with published in vivo results and require further study.
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Affiliation(s)
- Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States.
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Mary D Strem
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
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13
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Koch RA, Aime MC. Population structure of
Guyanagaster necrorhizus
supports termite dispersal for this enigmatic fungus. Mol Ecol 2018; 27:2667-2679. [PMID: 29729049 DOI: 10.1111/mec.14710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/07/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Rachel A. Koch
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
| | - M. Catherine Aime
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
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14
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Mustiga GM, Gezan SA, Phillips-Mora W, Arciniegas-Leal A, Mata-Quirós A, Motamayor JC. Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population. FRONTIERS IN PLANT SCIENCE 2018; 9:808. [PMID: 29971076 PMCID: PMC6018478 DOI: 10.3389/fpls.2018.00808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/25/2018] [Indexed: 05/21/2023]
Abstract
A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant (p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (-0.674, -0.690), respectively. Specific combining abilities for yield had significant (p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (-0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 (p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.
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Affiliation(s)
| | - Salvador A. Gezan
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Wilbert Phillips-Mora
- Tropical Agricultural Research and Higher Education Center (CATIE), Turrialba, Costa Rica
| | | | - Allan Mata-Quirós
- Tropical Agricultural Research and Higher Education Center (CATIE), Turrialba, Costa Rica
| | - Juan C. Motamayor
- Mars Incorporated, Miami, FL, United States
- *Correspondence: Juan C. Motamayor
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15
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Romero Luna MP, Aime MC, Chilvers MI, Wise KA. Genetic Diversity of Stenocarpella maydis in the Major Corn Production Areas of the United States. PLANT DISEASE 2017; 101:2020-2026. [PMID: 30677369 DOI: 10.1094/pdis-02-17-0292-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The fungus Stenocarpella maydis (Berk.) B. Sutton, causal agent of Diplodia ear rot, is a prevalent corn (Zea mays L.) pathogen in the United States. Although S. maydis reduces grain quality, causes yield loss, and can produce mycotoxins in some countries, few studies have examined its biology and genetic diversity. We analyzed the genetic diversity of 174 S. maydis isolates sampled across the major corn production areas in the United States using nine different microsatellites. In all, 55 unique multilocus genotypes (MLG) were observed out of the 174 S. maydis isolates tested. After conducting a Bayesian clustering analysis by STRUCTURE, it was observed that the most probable number of genetic groups was two; however, no separation by their geographical location was identified. According to the minimum spanning network, the S. maydis population is linked across geographic regions of the United States but also contains private genotypes. Temporal diversity in the inoculum source was also observed at one location across 4 years. The haploid stage of S. maydis was confirmed and both mating type genes were amplified among selected isolates with unique MLG. We theorize that, although S. maydis is primarily an asexual fungus, sporadic cryptic recombination may occur, which could contribute to the genetic diversity observed in this study.
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Affiliation(s)
- Martha P Romero Luna
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
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16
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Coelho MA, Bakkeren G, Sun S, Hood ME, Giraud T. Fungal Sex: The Basidiomycota. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0046-2016. [PMID: 28597825 PMCID: PMC5467461 DOI: 10.1128/microbiolspec.funk-0046-2016] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Indexed: 12/29/2022] Open
Abstract
Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation. Independent segregation of the two compatibility factors can create four haploid mating genotypes from meiosis, referred to as tetrapolarity. This condition is thought to be ancestral to the basidiomycetes. Alternatively, cosegregation by linkage of the two mating factors, or in some cases the absence of the pheromone-based discrimination, yields only two mating types from meiosis, referred to as bipolarity. Several species are now known to have large and highly rearranged chromosomal regions linked to mating-type genes. At the population level, polymorphism of the mating-type genes is an exceptional aspect of some basidiomycete fungi, where selection under outcrossing for rare, intercompatible allelic variants is thought to be responsible for numbers of mating types that may reach several thousand. Advances in genome sequencing and assembly are yielding new insights by comparative approaches among and within basidiomycete species, with the promise to resolve the evolutionary origins and dynamics of mating compatibility genetics in this major eukaryotic lineage.
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Affiliation(s)
- Marco A. Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre Summerland, BC, V0H 1Z0, Canada
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael E. Hood
- Department of Biology, Amherst College, 01002-5000 Amherst, Massachusetts, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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17
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Saprotrophic proteomes of biotypes of the witches' broom pathogen Moniliophthora perniciosa. Fungal Biol 2017; 121:743-753. [PMID: 28800846 DOI: 10.1016/j.funbio.2017.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/03/2017] [Accepted: 05/16/2017] [Indexed: 11/23/2022]
Abstract
Nine geographically diverse Moniliophthora perniciosa (witches' broom disease pathogen) isolates were cultured in vitro. They included six C-biotypes differing in virulence on cacao (Theobroma cacao), two S-biotypes (solanaceous hosts), and an L-biotype (liana hosts). Mycelial growth rates and morphologies differed considerably, but no characters were observed to correlate with virulence or biotype. In plant inoculations using basidiospores, one C-biotype caused symptoms on tomato (an S-biotype host), adding to evidence of limited host adaptation in these biotypes. Mycelial proteomes were analysed by two-dimensional gel electrophoresis (2-DE), and 619 gel spots were indexed on all replicate gels of at least one strain. Multivariate analysis of gel spots discriminated the L-biotype, but not the S-biotypes, from the remaining strains. The proteomic similarity of the S- and C-biotypes is consistent with their reported lack of phylogenetic distinction. Sequences from tandem mass spectrometry of tryptic peptides from major 2-DE spots were matched with Moniliophthora genome and transcript sequences on NCBI and WBD Transcriptome Atlas databases. Protein-spot identifications indicated that M. perniciosa saprotrophic mycelial proteomes expressed functions potentially connected with a 'virulence life-style', including peroxiredoxin, heat-shock proteins, nitrilase, formate dehydrogenase, a prominent complement of aldo-keto reductases, mannitol-1-phosphate dehydrogenase, and central metabolism enzymes with proposed pathogenesis functions.
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18
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Romero Navarro JA, Phillips-Mora W, Arciniegas-Leal A, Mata-Quirós A, Haiminen N, Mustiga G, Livingstone III D, van Bakel H, Kuhn DN, Parida L, Kasarskis A, Motamayor JC. Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases. FRONTIERS IN PLANT SCIENCE 2017; 8:1905. [PMID: 29184558 PMCID: PMC5694496 DOI: 10.3389/fpls.2017.01905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/23/2017] [Indexed: 05/08/2023]
Abstract
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.
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Affiliation(s)
| | | | | | - Allan Mata-Quirós
- Tropical Agricultural Research and Higher Education Center, Turrialba, Costa Rica
| | - Niina Haiminen
- IBM Thomas J. Watson Research Center, New York, NY, United States
| | | | | | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - David N. Kuhn
- Subtropical Horticulture Research Station, United States Department of Agriculture-Agricultural Research Service, Miami, FL, United States
| | - Laxmi Parida
- IBM Thomas J. Watson Research Center, New York, NY, United States
| | - Andrew Kasarskis
- Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - Juan C. Motamayor
- Mars Incorporated, Miami, FL, United States
- *Correspondence: Juan C. Motamayor
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19
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The cacao pathogen Moniliophthora roreri (Marasmiaceae) produces rhexolytic thallic conidia and their size is influenced by nuclear condition. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2016.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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