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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [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: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, Brar GS. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles. BMC Biol 2023; 21:233. [PMID: 37880702 PMCID: PMC10601111 DOI: 10.1186/s12915-023-01717-9] [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: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. RESULTS We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. CONCLUSIONS These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
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Affiliation(s)
- Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - John Hubensky
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Ramandeep Bamrah
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dinah Qutob
- Kent State University, Stark Campus, North Canton, OH, USA
| | - Mei-Lan de Graaf
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Sang Hu Kim
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Hadley R Kutcher
- Department of Plant Science/Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada (AAFC), Brandon Research and Development Center, Brandon, MB, Canada
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada (AAFC), Lethbridge Research and Development Center, Lethbridge, AB, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Keith Uloth
- British Columbia Pest Monitoring Network, Dawson Creek, BC, Canada
| | - Rishi R Burlakoti
- Agriculture and Agri-Food Canada (AAFC), Agassiz Research and Development Center, Agassiz, BC, Canada
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
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Abstract
Investigation of fungal biology has been frequently motivated by the fact that many fungal species are important plant and animal pathogens. Such efforts have contributed significantly toward our understanding of fungal pathogenic lifestyles (virulence factors and strategies) and the interplay with host immune systems. In parallel, work on fungal allorecognition systems leading to the characterization of fungal regulated cell death determinants and pathways, has been instrumental for the emergent concept of fungal immunity. The uncovered evolutionary trans-kingdom parallels between fungal regulated cell death pathways and innate immune systems incite us to reflect further on the concept of a fungal immune system. Here, I briefly review key findings that have shaped the fungal immunity paradigm, providing a perspective on what I consider its most glaring knowledge gaps. Undertaking to fill such gaps would establish firmly the fungal immune system inside the broader field of comparative immunology.
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Affiliation(s)
- Asen Daskalov
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Corresponding author
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Ke YH, Branco S, Bazzicalupo AL, Nguyen NH, Liao HL, Kennedy P, Bruns TD, Kuo A, LaButti K, Barry K, Grigoriev I, Vilgalys R. Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi. Genetics 2023; 224:iyad069. [PMID: 37070772 PMCID: PMC10213496 DOI: 10.1093/genetics/iyad069] [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: 02/24/2023] [Revised: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023] Open
Abstract
Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.
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Affiliation(s)
- Yi-Hong Ke
- Biology Department, Duke University, 130 Science Dr, Durham, NC 27708, USA
| | - Sara Branco
- Integrative Biology, University of Colorado, 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Anna L Bazzicalupo
- Department of Zoology, University of British Columbia, 4200—6270 University Blvd, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd, Quincy, FL 32351, USA
- Soil and Water Sciences Department, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor Grigoriev
- Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Rytas Vilgalys
- Biology Department, Duke University, 130 Science Dr, Durham, NC 27708, USA
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Shekarriz E, Chen J, Xu Z, Liu H. Disentangling the Functional Role of Fungi in Cold Seep Sediment. Microbiol Spectr 2023; 11:e0197822. [PMID: 36912690 PMCID: PMC10100914 DOI: 10.1128/spectrum.01978-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/22/2022] [Indexed: 03/14/2023] Open
Abstract
Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.
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Affiliation(s)
- Erfan Shekarriz
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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Vittorelli N, Rodríguez de la Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE. Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet 2023; 19:e1010347. [PMID: 36763677 PMCID: PMC9949647 DOI: 10.1371/journal.pgen.1010347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.
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Affiliation(s)
- Nina Vittorelli
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | | | - Alodie Snirc
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Emilie Levert
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Christophe Lalanne
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Elsa De Filippo
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fanny E. Hartmann
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
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Park MJ, Kim E, Jeong YS, Son MY, Jang Y, Ka KH. Determination and Analysis of Hyper-Variable A Mating Types in Wild Strains of Lentinula edodes in Korea. MYCOBIOLOGY 2023; 51:26-35. [PMID: 36846627 PMCID: PMC9946336 DOI: 10.1080/12298093.2022.2161157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
The diversity of A mating type in wild strains of Lentinula edodes was extensively analyzed to characterize and utilize them for developing new cultivars. One hundred twenty-three A mating type alleles, including 67 newly discovered alleles, were identified from 106 wild strains collected for the past four decades in Korea. Based on previous studies and current findings, a total of 130 A mating type alleles have been found, 124 of which were discovered from wild strains, indicating the hyper-variability of A mating type alleles of L. edodes. About half of the A mating type alleles in wild strains were found in more than two strains, whereas the other half of the alleles were found in only one strain. About 90% of A mating type combinations in dikaryotic wild strains showed a single occurrence. Geographically, diverse A mating type alleles were intensively located in the central region of the Korean peninsula, whereas only allele A17 was observed throughout Korea. We also found the conservation of the TCCCAC motif in addition to the previously reported motifs, including ATTGT, ACAAT, and GCGGAG, in the intergenic regions of A mating loci. Sequence comparison among some alleles indicated that accumulated mutation and recombination would contribute to the diversification of A mating type alleles in L. edodes. Our data support the rapid evolution of A mating locus in L. edodes, and would help to understand the characteristics of A mating loci of wild strains in Korea and help to utilize them for developing new cultivars.
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Affiliation(s)
- Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Eunjin Kim
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Yeun Sug Jeong
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Mi-Young Son
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Yeongseon Jang
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Kang-Hyeon Ka
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
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8
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Origin and persistence of polymorphism in loci targeted by disassortative preference: a general model. J Math Biol 2022; 86:4. [PMID: 36441252 DOI: 10.1007/s00285-022-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022]
Abstract
The emergence and persistence of polymorphism within populations generally requires specific regimes of natural or sexual selection. Here, we develop a unified theoretical framework to explore how polymorphism at targeted loci can be generated and maintained by either disassortative mating choice or balancing selection due to, for example, heterozygote advantage. To this aim, we model the dynamics of alleles at a single locus A in a population of haploid individuals, where reproductive success depends on the combination of alleles carried by the parents at locus A. Our theoretical study of the model confirms that the conditions for the persistence of a given level of allelic polymorphism depend on the relative reproductive advantages among pairs of individuals. Interestingly, equilibria with unbalanced allelic frequencies were shown to emerge from successive introduction of mutants. We then investigate the role of the function linking allelic divergence to reproductive advantage on the evolutionary fate of alleles within the population. Our results highlight the significance of the shape of this function for both the number of alleles maintained and their level of genetic divergence. Large number of alleles are maintained with substantial replacement of alleles, when disassortative advantage slowly increases with allelic differentiation . In contrast, few highly differentiated alleles are predicted to be maintained when genetic differentiation has a strong effect on disassortative advantage. These opposite effects predicted by our model explain how disassortative mate choice may lead to various levels of allelic differentiation and polymorphism, and shed light on the effect of mate preferences on the persistence of balanced and unbalanced polymorphism in natural population.
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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10
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Carpentier F, Rodríguez de la Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood ME, Giraud T. Tempo of degeneration across independently evolved non-recombining regions. Mol Biol Evol 2022; 39:6553583. [PMID: 35325190 PMCID: PMC9004411 DOI: 10.1093/molbev/msac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in nonrecombining regions, that is, the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of nonoptimal codons and nonsynonymous substitutions in nonrecombining regions. We found a reduced frequency of optimal codons in the nonrecombining regions compared with autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared with recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca. 3 Ma. The strength of purifying selection remained virtually constant at dN/dS = 0.55, that is, at an intermediate level between purifying selection and neutral evolution. Accordingly, nonsynonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per My. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in nonrecombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.
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Affiliation(s)
- Fantin Carpentier
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Université de Lille, CNRS, UMR 8198-Evo-Eco-Paleo F-59000, Lille, France
| | - Ricardo C. Rodríguez de la Vega
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
| | - Paul Jay
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Marine Duhamel
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jacqui A. Shykoff
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Michael H. Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | - R. Margaret Wallen
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | | | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
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11
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Wang G, Wang Y, Chen L, Wang H, Guo L, Zhou X, Dou M, Wang B, Lin J, Liu L, Wang Z, Deng Y, Zhang J. Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus. IMA Fungus 2021; 12:35. [PMID: 34930496 PMCID: PMC8686365 DOI: 10.1186/s43008-021-00086-8] [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: 07/29/2021] [Accepted: 12/15/2021] [Indexed: 11/12/2022] Open
Abstract
The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.
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Affiliation(s)
- Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers University, Yancheng, 224002 China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuanyuan Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lianfu Chen
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430000 China
| | - Hongbo Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Guo
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuan Zhou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meijie Dou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jingxian Lin
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lei Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, 350002 China
| | - Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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12
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Clergeot PH, Olson Å. Mitonuclear Genetic Interactions in the Basidiomycete Heterobasidion parviporum Involve a Non-conserved Mitochondrial Open Reading Frame. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:779337. [PMID: 37744141 PMCID: PMC10512249 DOI: 10.3389/ffunb.2021.779337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/19/2021] [Indexed: 09/26/2023]
Abstract
The mitochondrial and nuclear genomes of Eukaryotes are inherited separately and consequently follow distinct evolutionary paths. Nevertheless, the encoding of many mitochondrial proteins by the nuclear genome shows the high level of integration they have reached, which makes mitonuclear genetic interactions all the more conceivable. For each species, natural selection has fostered the evolution of coadapted alleles in both genomes, but a population-wise divergence of such alleles could lead to important phenotypic variation, and, ultimately, to speciation. In this study in the Basidiomycete Heterobasidion parviporum, we have investigated the genetic basis of phenotypic variation among laboratory-designed heterokaryons carrying the same pair of haploid nuclei, but a different mitochondrial genome. Radial growth rate data of thirteen unrelated homokaryotic parents and of their heterokaryotic offspring were combined with SNP data extracted from parental genome sequences to identify nuclear and mitochondrial loci involved in mitonuclear interactions. Two nuclear loci encoding mitochondrial proteins appeared as best candidates to engage in a genetic interaction affecting radial growth rate with a non-conserved mitochondrial open reading frame of unknown function and not reported apart from the Russulales order of Basidiomycete fungi. We believe our approach could be useful to investigate several important traits of fungal biology where mitonuclear interactions play a role, including virulence of fungal pathogens.
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Affiliation(s)
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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13
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Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis. Microbiol Mol Biol Rev 2021; 86:e0001921. [PMID: 34817241 DOI: 10.1128/mmbr.00019-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.
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14
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Wu JQ, Song L, Ding Y, Dong C, Hasan M, Park RF. A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution. Front Microbiol 2021; 12:704253. [PMID: 34394053 PMCID: PMC8358450 DOI: 10.3389/fmicb.2021.704253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022] Open
Abstract
Despite the global economic importance of the wheat leaf rust pathogen Puccinia triticina (Pt), genomic resources for Pt are limited and chromosome-level assemblies of Pt are lacking. Here, we present a complete haplotype-resolved genome assembly at a chromosome-scale for Pt using the Australian pathotype 64-(6),(7),(10),11 (Pt64; North American race LBBQB) built upon the newly developed technologies of PacBio and Hi-C sequencing. PacBio reads with ∼200-fold coverage (29.8 Gb data) were assembled by Falcon and Falcon-unzip and subsequently scaffolded with Hi-C data using Falcon-phase and Proximo. This approach allowed us to construct 18 chromosome pseudomolecules ranging from 3.5 to 12.3 Mb in size for each haplotype of the dikaryotic genome of Pt64. Each haplotype had a total length of ∼147 Mb, scaffold N 50 of ∼9.4 Mb, and was ∼93% complete for BUSCOs. Each haplotype had ∼29,800 predicted genes, of which ∼2,000 were predicted as secreted proteins (SPs). The investigation of structural variants (SVs) between haplotypes A and B revealed that 10% of the total genome was spanned by SVs, highlighting variations previously undetected by short-read based assemblies. For the first time, the mating type (MAT) genes on each haplotype of Pt64 were identified, which showed that MAT loci a and b are located on two chromosomes (chromosomes 7 and 14), representing a tetrapolar type. Furthermore, the Pt64 assembly enabled haplotype-based evolutionary analyses for 21 Australian Pt isolates, which highlighted the importance of a haplotype resolved reference when inferring genetic relationships using whole genome SNPs. This Pt64 assembly at chromosome-scale with full phase information provides an invaluable resource for genomic and evolutionary research, which will accelerate the understanding of molecular mechanisms underlying Pt-wheat interactions and facilitate the development of durable resistance to leaf rust in wheat and sustainable control of rust disease.
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Affiliation(s)
| | | | | | | | | | - Robert F. Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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15
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Abstract
True morels (Morchella spp., Morchellaceae, Ascomycota) are widely regarded as a highly prized delicacy and are of great economic and scientific value. Recently, the rapid development of cultivation technology and expansion of areas for artificial morel cultivation have propelled morel research into a hot topic. Many studies have been conducted in various aspects of morel biology, but despite this, cultivation sites still frequently report failure to fruit or only low production of fruiting bodies. Key problems include the gap between cultivation practices and basic knowledge of morel biology. In this review, in an effort to highlight the mating systems, evolution, and life cycle of morels, we summarize the current state of knowledge of morel sexual reproduction, the structure and evolution of mating-type genes, the sexual process itself, and the influence of mating-type genes on the asexual stages and conidium production. Understanding of these processes is critical for improving technology for the cultivation of morels and for scaling up their commercial production. Morel species may well be good candidates as model species for improving sexual development research in ascomycetes in the future.
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16
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Foulongne-Oriol M, Taskent O, Kües U, Sonnenberg ASM, van Peer AF, Giraud T. Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus. Genes (Basel) 2021; 12:1079. [PMID: 34356095 PMCID: PMC8305134 DOI: 10.3390/genes12071079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.
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Affiliation(s)
| | - Ozgur Taskent
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Goettingen Center for Molecular Biosciences (GZMB), Büsgen-Institute, University of Goettingen, Büsgenweg 2, 37077 Goettingen, Germany;
| | - Anton S. M. Sonnenberg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Arend F. van Peer
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
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17
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Early Identification of Root Rot Disease by Using Hyperspectral Reflectance: The Case of Pathosystem Grapevine/Armillaria. REMOTE SENSING 2021. [DOI: 10.3390/rs13132436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Armillaria genus represents one of the most common causes of chronic root rot disease in woody plants. Prompt recognition of diseased plants is crucial to control the pathogen. However, the current disease detection methods are limited at a field scale. Therefore, an alternative approach is needed. In this study, we investigated the potential of hyperspectral techniques to identify fungi-infected vs. healthy plants of Vitis vinifera. We used the hyperspectral imaging sensor Specim-IQ to acquire leaves’ reflectance data of the Teroldego Rotaliano grapevine cultivar. We analyzed three different groups of plants: healthy, asymptomatic, and diseased. Highly significant differences were found in the near-infrared (NIR) spectral region with a decreasing pattern from healthy to diseased plants attributable to the leaf mesophyll changes. Asymptomatic plants emerged from the other groups due to a lower reflectance in the red edge spectrum (around 705 nm), ascribable to an accumulation of secondary metabolites involved in plant defense strategies. Further significant differences were observed in the wavelengths close to 550 nm in diseased vs. asymptomatic plants. We evaluated several machine learning paradigms to differentiate the plant groups. The Naïve Bayes (NB) algorithm, combined with the most discriminant variables among vegetation indices and spectral narrow bands, provided the best results with an overall accuracy of 90% and 75% in healthy vs. diseased and healthy vs. asymptomatic plants, respectively. To our knowledge, this study represents the first report on the possibility of using hyperspectral data for root rot disease diagnosis in woody plants. Although further validation studies are required, it appears that the spectral reflectance technique, possibly implemented on unmanned aerial vehicles (UAVs), could be a promising tool for a cost-effective, non-invasive method of Armillaria disease diagnosis and mapping in-field, contributing to a significant step forward in precision viticulture.
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18
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Paganini J, Pontarotti P. Search for MHC/TCR-Like Systems in Living Organisms. Front Immunol 2021; 12:635521. [PMID: 34017326 PMCID: PMC8129030 DOI: 10.3389/fimmu.2021.635521] [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: 11/30/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Highly polymorphic loci evolved many times over the history of species. These polymorphic loci are involved in three types of functions: kind recognition, self-incompatibility, and the jawed vertebrate adaptive immune system (AIS). In the first part of this perspective, we reanalyzed and described some cases of polymorphic loci reported in the literature. There is a convergent evolution within each functional category and between functional categories, suggesting that the emergence of these self/non-self recognition loci has occurred multiple times throughout the evolutionary history. Most of the highly polymorphic loci are coding for proteins that have a homophilic interaction or heterophilic interaction between linked loci, leading to self or non-self-recognition. The highly polymorphic MHCs, which are involved in the AIS have a different functional mechanism, as they interact through presented self or non-self-peptides with T cell receptors, whose diversity is generated by somatic recombination. Here we propose a mechanism called “the capacity of recognition competition mechanism” that might contribute to the evolution of MHC polymorphism. We propose that the published cases corresponding to these three biological categories represent a small part of what can be found throughout the tree of life, and that similar mechanisms will be found many times, including the one where polymorphic loci interact with somatically generated loci.
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Affiliation(s)
| | - Pierre Pontarotti
- XEGEN, Gemenos, France.,Aix Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.,SNC5039 CNRS, Marseille, France
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19
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Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne‐Oriol M, Silar P, Malagnac F, Grognet P, Giraud T. Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. THE NEW PHYTOLOGIST 2021; 229:2470-2491. [PMID: 33113229 PMCID: PMC7898863 DOI: 10.1111/nph.17039] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/03/2020] [Indexed: 05/08/2023]
Abstract
Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.
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Affiliation(s)
- Fanny E. Hartmann
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Marine Duhamel
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
- Ruhr‐Universität Bochum, Evolution of Plants and Fungi ‐ Gebäude ND 03/174Universitätsstraße150, 44801 BochumGermany
| | - Fantin Carpentier
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Michael E. Hood
- Biology Department, Science CentreAmherst CollegeAmherstMA01002USA
| | | | - Philippe Silar
- Lab Interdisciplinaire Energies DemainUniv Paris DiderotSorbonne Paris CiteParis 13F‐75205France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Tatiana Giraud
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
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20
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Kämper J, Friedrich MW, Kahmann R. Creating novel specificities in a fungal nonself recognition system by single step homologous recombination events. THE NEW PHYTOLOGIST 2020; 228:1001-1010. [PMID: 32559311 DOI: 10.1111/nph.16755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
In many organisms, two component systems have evolved to discriminate self from nonself. While the molecular function of the two components has been elucidated in several systems, the evolutionary events leading to the large number of different specificities for self-nonself recognition found in most systems remain obscure. We have investigated the variation within a multiallelic nonself recognition system in the phytopathogenic basidiomycete Ustilago maydis by means of sequence analysis and functional studies. The multiallelic b mating type locus of U. maydis ensures outbreeding during sexual development. Nonself recognition is specified by the two homeodomain proteins, bE and bW, encoded by the b locus. While bE-bW combinations from the same allele do not dimerize, bE and bW proteins originating from different alleles form a heterodimeric complex that functions as master regulator for sexual and pathogenic development. We show that novel specificities of the b mating type locus have arisen by single homologous recombination events between distinct b alleles that lead to a simultaneous exchange of subdomains involved in dimerization in both bE and bW, altering the specificity of both proteins in a single step.
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Affiliation(s)
- Jörg Kämper
- Department Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, 35043, Germany
- Department of Genetics, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz Haber Weg 4, Karlsruhe, 76131, Germany
| | - Michael W Friedrich
- Department Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, 35043, Germany
- Microbial Ecophysiology Group BreMarE, University of Bremen, Leobener Straße 3, Bremen, 28359, Germany
| | - Regine Kahmann
- Department Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, 35043, Germany
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21
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Redr D, Dahlberg A, Stenlid J, Sunhede S, Vasaitis R, Menkis A. The mating type system of the rare polypore Hapalopilus croceus. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. G3-GENES GENOMES GENETICS 2019; 9:3057-3066. [PMID: 31371382 PMCID: PMC6778795 DOI: 10.1534/g3.119.400563] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as 'Heirloom'. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60-70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.
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Czuppon P, Constable GWA. Invasion and Extinction Dynamics of Mating Types Under Facultative Sexual Reproduction. Genetics 2019; 213:567-580. [PMID: 31391266 PMCID: PMC6781889 DOI: 10.1534/genetics.119.302306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/04/2019] [Indexed: 01/08/2023] Open
Abstract
In sexually reproducing isogamous species, syngamy between gametes is generally not indiscriminate, but rather restricted to occurring between complementary self-incompatible mating types. A longstanding question regards the evolutionary pressures that control the number of mating types observed in natural populations, which ranges from two to many thousands. Here, we describe a population genetic null model of this reproductive system, and derive expressions for the stationary probability distribution of the number of mating types, the establishment probability of a newly arising mating type, and the mean time to extinction of a resident type. Our results yield that the average rate of sexual reproduction in a population correlates positively with the expected number of mating types observed. We further show that the low number of mating types predicted in the rare-sex regime is primarily driven by low invasion probabilities of new mating type alleles, with established resident alleles being very stable over long evolutionary periods. Moreover, our model naturally exhibits varying selection strength dependent on the number of resident mating types. This results in higher extinction and lower invasion rates for an increasing number of residents.
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Affiliation(s)
- Peter Czuppon
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, 75231 Paris, France
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, 75252 Paris, France
| | - George W A Constable
- Department of Mathematical Sciences, The University of Bath, BA2 7AY, United Kingdom
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24
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Czuppon P, Rogers DW. Evolution of mating types in finite populations: The precarious advantage of being rare. J Evol Biol 2019; 32:1290-1299. [PMID: 31479547 DOI: 10.1111/jeb.13528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/28/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023]
Abstract
Sexually reproducing populations with self-incompatibility bear the cost of limiting potential mates to individuals of a different type. Rare mating types escape this cost since they are unlikely to encounter incompatible partners, leading to the deterministic prediction of continuous invasion by new mutants and an ever-increasing number of types. However, rare types are also at an increased risk of being lost by random drift. Calculating the number of mating types that a population can maintain requires consideration of both the deterministic advantages and the stochastic risks. By comparing the relative importance of selection and drift, we show that a population of size N can maintain a maximum of approximately N1/3 mating types for intermediate population sizes, whereas for large N, we derive a formal estimate. Although the number of mating types in a population is quite stable, the rare-type advantage promotes turnover of types. We derive explicit formulas for both the invasion and turnover probabilities in finite populations.
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Affiliation(s)
- Peter Czuppon
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre Interdisciplinaire de Recherche en Biologie, CNRS Collège de France, PSL Research University, Paris, France.,Institut d'Ecologie et des Sciences de l'Environnement (IEES), UPEC, CNRS, IRD, INRA, Sorbonne Université, Paris, France
| | - David W Rogers
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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25
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Sun S, Coelho MA, Heitman J, Nowrousian M. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 2019; 15:e1008365. [PMID: 31490920 PMCID: PMC6730849 DOI: 10.1371/journal.pgen.1008365] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:431-457. [PMID: 31337277 DOI: 10.1146/annurev-phyto-082718-095947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | | | - Fantin Carpentier
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | - Pierre Gladieux
- UMR BGPI, Univ. Montpellier, INRA, CIRAD, Montpellier SupAgro, 34398 Montpellier, France
| | - Amandine Cornille
- Génétique Quantitative et Evolution-Le Moulon, INRA; Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, Massachusetts 01002-5000, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
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27
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Passer AR, Coelho MA, Billmyre RB, Nowrousian M, Mittelbach M, Yurkov AM, Averette AF, Cuomo CA, Sun S, Heitman J. Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens. mBio 2019; 10:e00764-19. [PMID: 31186317 PMCID: PMC6561019 DOI: 10.1128/mbio.00764-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022] Open
Abstract
Speciation is a central mechanism of biological diversification. While speciation is well studied in plants and animals, in comparison, relatively little is known about speciation in fungi. One fungal model is the Cryptococcus genus, which is best known for the pathogenic Cryptococcus neoformans/Cryptococcus gattii species complex that causes >200,000 new human infections annually. Elucidation of how these species evolved into important human-pathogenic species remains challenging and can be advanced by studying the most closely related nonpathogenic species, Cryptococcus amylolentus and Tsuchiyaea wingfieldii However, these species have only four known isolates, and available data were insufficient to determine species boundaries within this group. By analyzing full-length chromosome assemblies, we reappraised the phylogenetic relationships of the four available strains, confirmed the genetic separation of C. amylolentus and T. wingfieldii (now Cryptococcus wingfieldii), and revealed an additional cryptic species, for which the name Cryptococcus floricola is proposed. The genomes of the three species are ∼6% divergent and exhibit significant chromosomal rearrangements, including inversions and a reciprocal translocation that involved intercentromeric ectopic recombination, which together likely impose significant barriers to genetic exchange. Using genetic crosses, we show that while C. wingfieldii cannot interbreed with any of the other strains, C. floricola can still undergo sexual reproduction with C. amylolentus However, most of the resulting spores were inviable or sterile or showed reduced recombination during meiosis, indicating that intrinsic postzygotic barriers had been established. Our study and genomic data will foster additional studies addressing fungal speciation and transitions between nonpathogenic and pathogenic Cryptococcus lineages.IMPORTANCE The evolutionary drivers of speciation are critical to our understanding of how new pathogens arise from nonpathogenic lineages and adapt to new environments. Here we focus on the Cryptococcus amylolentus species complex, a nonpathogenic fungal lineage closely related to the human-pathogenic Cryptococcus neoformans/Cryptococcus gattii complex. Using genetic and genomic analyses, we reexamined the species boundaries of four available isolates within the C. amylolentus complex and revealed three genetically isolated species. Their genomes are ∼6% divergent and exhibit chromosome rearrangements, including translocations and small-scale inversions. Although two of the species (C. amylolentus and newly described C. floricola) were still able to interbreed, the resulting hybrid progeny were usually inviable or sterile, indicating that barriers to reproduction had already been established. These results advance our understanding of speciation in fungi and highlight the power of genomics in assisting our ability to correctly identify and discriminate fungal species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Moritz Mittelbach
- Geobotany, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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28
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Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes ( Microbotryum lychnidis-dioicae). G3-GENES GENOMES GENETICS 2019; 9:1987-1998. [PMID: 31015196 PMCID: PMC6553529 DOI: 10.1534/g3.119.400242] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recombination suppression on sex chromosomes often extends in a stepwise manner, generating evolutionary strata of differentiation between sex chromosomes. Sexual antagonism is a widely accepted explanation for evolutionary strata, postulating that sets of genes beneficial in only one sex are successively linked to the sex-determining locus. The anther-smut fungus Microbotryum lychnidis-dioicae has mating-type chromosomes with evolutionary strata, only some of which link mating-type genes. Male and female roles are non-existent in this fungus, but mating-type antagonistic selection can also generate evolutionary strata, although the life cycle of the fungus suggests it should be restricted to few traits. Here, we tested the hypothesis that mating-type antagonism may have triggered recombination suppression beyond mating-type genes in M. lychnidis-dioicae by searching for footprints of antagonistic selection in evolutionary strata not linking mating-type loci. We found that these evolutionary strata (i) were not enriched in genes upregulated in the haploid phase, where cells are of alternative mating types, (ii) carried no gene differentially expressed between mating types, and (iii) carried no genes displaying footprints of specialization in terms of protein sequences (dN/dS) between mating types after recommended filtering. Without filtering, eleven genes showed signs of positive selection in the strata not linking mating-type genes, which constituted an enrichment compared to autosomes, but their functions were not obviously involved in antagonistic selection. Thus, we found no strong evidence that antagonistic selection has contributed to extending recombination suppression beyond mating-type genes. Alternative hypotheses should therefore be explored to improve our understanding of the sex-related chromosome evolution.
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29
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Carpentier F, Rodríguez de la Vega RC, Branco S, Snirc A, Coelho MA, Hood ME, Giraud T. Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi. Genome Res 2019; 29:944-953. [PMID: 31043437 PMCID: PMC6581054 DOI: 10.1101/gr.242578.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/29/2019] [Indexed: 12/28/2022]
Abstract
The degree of selfing has major impacts on adaptability and is often controlled by molecular mechanisms determining mating compatibility. Changes in compatibility systems are therefore important evolutionary events, but their underlying genomic mechanisms are often poorly understood. Fungi display frequent shifts in compatibility systems, and their small genomes facilitate elucidation of the mechanisms involved. In particular, linkage between the pre- and postmating compatibility loci has evolved repeatedly, increasing the odds of gamete compatibility under selfing. Here, we studied the mating-type chromosomes of two anther-smut fungi with unlinked mating-type loci despite a self-fertilization mating system. Segregation analyses and comparisons of high-quality genome assemblies revealed that these two species displayed linkage between mating-type loci and their respective centromeres. This arrangement renders the same improved odds of gamete compatibility as direct linkage of the two mating-type loci under the automictic mating (intratetrad selfing) of anther-smut fungi. Recombination cessation was found associated with a large inversion in only one of the four linkage events. The lack of trans-specific polymorphism at genes located in nonrecombining regions and linkage date estimates indicated that the events of recombination cessation occurred independently in the two sister species. Our study shows that natural selection can repeatedly lead to similar genomic patterns and phenotypes, and that different evolutionary paths can lead to distinct yet equally beneficial responses to selection. Our study further highlights that automixis and gene linkage to centromeres have important genetic and evolutionary consequences, while being poorly recognized despite being present in a broad range of taxa.
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Affiliation(s)
- Fantin Carpentier
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Sara Branco
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Marco A Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, Massachusetts 01002, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
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30
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Nieuwenhuis BPS, Aanen DK. Nuclear arms races: Experimental evolution for mating success in the mushroom-forming fungus Schizophyllum commune. PLoS One 2018; 13:e0209671. [PMID: 30589876 PMCID: PMC6320016 DOI: 10.1371/journal.pone.0209671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
When many gametes compete to fertilize a limited number of compatible gametes, sexual selection will favour traits that increase competitive success during mating. In animals and plants, sperm and pollen competition have yielded many interesting adaptations for improved mating success. In fungi, similar processes have not been shown directly yet. We test the hypothesis that sexual selection can increase competitive fitness during mating, using experimental evolution in the mushroom-forming fungus Schizophyllum commune (Basidiomycota). Mating in mushroom fungi occurs by donation of nuclei to a mycelium. These fertilizing 'male' nuclei migrate through the receiving 'female' mycelium. In our setup, an evolving population of nuclei was serially mated with a non-evolving female mycelium for 20 sexual generations. From the twelve tested evolved lines, four had increased and one had decreased fitness relative to an unevolved competitor. Even though only two of those five remained significant after correcting for multiple comparisons, for all five lines we found a correlation between the efficiency with which the female mycelium is accessed and fitness, providing additional circumstantial evidence for fitness change in those five lines. In two lines, fitness change was also accompanied by increased spore production. The one line with net reduced competitive fitness had increased spore production, but reduced fertilisation efficiency. We did not find trade-offs between male reproductive success and other fitness components. We compare these findings with examples of sperm and pollen competition and show that many similarities between these systems and nuclear competition in mushrooms exist.
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Affiliation(s)
- Bart P. S. Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Duur K. Aanen
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
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31
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Snyder AB, Biango-Daniels MN, Hodge KT, Worobo RW. Nature Abhors a Vacuum: Highly Diverse Mechanisms Enable Spoilage Fungi to Disperse, Survive, and Propagate in Commercially Processed and Preserved Foods. Compr Rev Food Sci Food Saf 2018; 18:286-304. [DOI: 10.1111/1541-4337.12403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Abigail B. Snyder
- the Dept. of Extension; The Ohio State Univ.; 1680 Madison Ave. Wooster OH 44691 USA
| | - Megan N. Biango-Daniels
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Kathie T. Hodge
- the Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science; Cornell Univ.; Ithaca NY 14850 USA
| | - Randy W. Worobo
- the Dept. of Food Science; Cornell Univ.; 411 Tower Rd. Ithaca NY 14850 USA
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Abstract
Aspergillus nidulans has long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genus Aspergillus, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings from Aspergillus, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction in A. nidulans was investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in the Pezizomycotina (e.g. AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (e.g. BrlA) had a more restricted distribution solely in the Eurotiomycetes, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of the Pezizomycotina. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of the A. nidulans abaA gene in Monascus ruber failed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of the Saccharomycotina supports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in the Pezizomycotina. Investigations were also made into the evolution of sex and sexuality in the aspergilli. MAT loci were identified from the heterothallic Aspergillus (Emericella) heterothallicus and Aspergillus (Neosartorya) fennelliae and the homothallic Aspergillus pseudoglaucus (=Eurotium repens). A consistent architecture of the MAT locus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement of MAT loci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made using A. clavatus as a representative 'asexual' species. It was possible to induce a sexual cycle in A. clavatus given the correct MAT1-1 and MAT1-2 partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexual reproduction might be possible in many supposedly asexual aspergilli and beyond, providing general insights into the nature of asexuality in fungi.
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The rate of facultative sex governs the number of expected mating types in isogamous species. Nat Ecol Evol 2018; 2:1168-1175. [DOI: 10.1038/s41559-018-0580-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/16/2018] [Indexed: 01/30/2023]
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Branco S, Carpentier F, Rodríguez de la Vega RC, Badouin H, Snirc A, Le Prieur S, Coelho MA, de Vienne DM, Hartmann FE, Begerow D, Hood ME, Giraud T. Multiple convergent supergene evolution events in mating-type chromosomes. Nat Commun 2018; 9:2000. [PMID: 29784936 PMCID: PMC5962589 DOI: 10.1038/s41467-018-04380-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 04/24/2018] [Indexed: 11/18/2022] Open
Abstract
Convergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their prevalence or evolution. A recent study on anther-smut fungi documented supergene formation by rearrangements linking two key mating-type loci, controlling pre- and post-mating compatibility. Here further high-quality genome assemblies reveal four additional independent cases of chromosomal rearrangements leading to regions of suppressed recombination linking these mating-type loci in closely related species. Such convergent transitions in genomic architecture of mating-type determination indicate strong selection favoring linkage of mating-type loci into cosegregating supergenes. We find independent evolutionary strata (stepwise recombination suppression) in several species, with extensive rearrangements, gene losses, and transposable element accumulation. We thus show remarkable convergence in mating-type chromosome evolution, recurrent supergene formation, and repeated evolution of similar phenotypes through different genomic changes. Supergenes result from beneficial linkage and recombination suppression between two or more genes. Giraud and colleagues use whole genome sequencing data to show convergent evolution of supergenes on mating-type chromosomes in multiple closely-related fungal lineages.
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Affiliation(s)
- Sara Branco
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Fantin Carpentier
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Hélène Badouin
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France.,Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Stéphanie Le Prieur
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Marco A Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Damien M de Vienne
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Dominik Begerow
- Ruhr-Universitat Bochum, AG Geobotanik Gebaude ND 03/174 Universitatsstraße, 15044780, Bochum, Germany
| | - Michael E Hood
- Department of Biology, University of Virginia, Gilmer 051, Charlottesville, VA, 22903, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France.
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Repeated evolution of self-compatibility for reproductive assurance. Nat Commun 2018; 9:1639. [PMID: 29691402 PMCID: PMC5915400 DOI: 10.1038/s41467-018-04054-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 01/22/2023] Open
Abstract
Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility. Mating-type switching enables self-compatible reproduction in fungi, but switching ability is variable even within species. Here, the authors find de novo evolution of switching genotypes in experimentally evolved fission yeast populations and show a trade-off between mating success and growth.
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Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. Proc Natl Acad Sci U S A 2017. [PMID: 28630332 DOI: 10.1073/pnas.1701658114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes can display successive steps of recombination suppression known as "evolutionary strata," which are thought to result from the successive linkage of sexually antagonistic genes to sex-determining genes. However, there is little evidence to support this explanation. Here we investigate whether evolutionary strata can evolve without sexual antagonism using fungi that display suppressed recombination extending beyond loci determining mating compatibility despite lack of male/female roles associated with their mating types. By comparing full-length chromosome assemblies from five anther-smut fungi with or without recombination suppression in their mating-type chromosomes, we inferred the ancestral gene order and derived chromosomal arrangements in this group. This approach shed light on the chromosomal fusion underlying the linkage of mating-type loci in fungi and provided evidence for multiple clearly resolved evolutionary strata over a range of ages (0.9-2.1 million years) in mating-type chromosomes. Several evolutionary strata did not include genes involved in mating-type determination. The existence of strata devoid of mating-type genes, despite the lack of sexual antagonism, calls for a unified theory of sex-related chromosome evolution, incorporating, for example, the influence of partially linked deleterious mutations and the maintenance of neutral rearrangement polymorphism due to balancing selection on sexes and mating types.
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Mujic AB, Kuo A, Tritt A, Lipzen A, Chen C, Johnson J, Sharma A, Barry K, Grigoriev IV, Spatafora JW. Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus. G3 (BETHESDA, MD.) 2017; 7:1775-1789. [PMID: 28450370 PMCID: PMC5473757 DOI: 10.1534/g3.117.039396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/28/2017] [Indexed: 12/04/2022]
Abstract
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)-the first genomes available for Basidiomycota truffles-and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A-locus as well as pheromone receptor and pheromone precursor homologs at the mating type B-locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B-locus pheromone receptor and precursor genes than R. vesiculosus, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B-locus compared to a single copy in R. vesiculosus Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B-locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B-locus region structure intermediate between bipolar and tetrapolar Boletales.
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Affiliation(s)
- Alija Bajro Mujic
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Alan Kuo
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Andrew Tritt
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Anna Lipzen
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Cindy Chen
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Jenifer Johnson
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Aditi Sharma
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Kerrie Barry
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Igor V Grigoriev
- Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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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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Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci. G3-GENES GENOMES GENETICS 2017; 7:361-376. [PMID: 27913634 PMCID: PMC5295586 DOI: 10.1534/g3.116.032797] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Three members of the Puccinia genus, Pucciniatriticina (Pt), Pstriiformis f.sp. tritici (Pst), and Pgraminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.
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Corradi N, Brachmann A. Fungal Mating in the Most Widespread Plant Symbionts? TRENDS IN PLANT SCIENCE 2017; 22:175-183. [PMID: 27876487 DOI: 10.1016/j.tplants.2016.10.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are relevant plant symbionts whose hyphae and spores carry hundreds of coexisting nuclei with supposedly divergent genomes but no sign of sexual reproduction. This unusual biology suggested that conventional fungal mating is not amendable to optimize strains for plant growth, but recent evidence of sexual-related nuclear inheritance in these organisms is now challenging this widespread notion. Here, we outline our knowledge of AMF genetics within a historical context, and discuss how past and new information in this area changed our understanding of AMF biology. We also highlight the mating-related processes in AMF, and propose new research avenues and approaches that could lead to a better application of these organisms for agricultural and environmental practices.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
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Fortuna TM, Snirc A, Badouin H, Gouzy J, Siguenza S, Esquerre D, Le Prieur S, Shykoff JA, Giraud T. Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing. PLoS One 2016; 11:e0165656. [PMID: 27832131 PMCID: PMC5104459 DOI: 10.1371/journal.pone.0165656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/14/2016] [Indexed: 01/06/2023] Open
Abstract
Background Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i.e., with two independently segregating mating-type loci), while most of the anther-smut Microbotryum fungi are bipolar (i.e., with a single mating-type locus). Saponaria officinalis is a widespread long-lived perennial plant species with multiple flowering stems, which makes its anther-smut pathogen a good model for studying phylogeography and within-host multiple infections. Principal Findings Here, based on a generated genome sequence of M. saponariae we developed 6 multiplexes with a total of 22 polymorphic microsatellite markers using an inexpensive and efficient method. We scored these markers in fungal individuals collected from 97 populations across Europe, and found that the number of their alleles ranged from 2 to 11, and their expected heterozygosity from 0.01 to 0.58. Cross-species amplification was examined using nine other Microbotryum species parasitizing hosts belonging to Silene, Dianthus and Knautia genera. All loci were successfully amplified in at least two other Microbotryum species. Significance These newly developed markers will provide insights into the population genetic structure and the occurrence of within-host multiple infections of M. saponariae. In addition, the draft genome of M. saponariae, as well as one of the described markers will be useful resources for studying the evolution of the breeding systems in the genus Microbotryum and the evolution of specialization onto different plant species.
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Affiliation(s)
- Taiadjana M. Fortuna
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
- * E-mail:
| | - Alodie Snirc
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Hélène Badouin
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Jérome Gouzy
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Diane Esquerre
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, F-31326, France
| | - Stéphanie Le Prieur
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Jacqui A. Shykoff
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Tatiana Giraud
- Laboratoire d’Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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Nieuwenhuis BPS, Immler S. The evolution of mating-type switching for reproductive assurance. Bioessays 2016; 38:1141-1149. [DOI: 10.1002/bies.201600139] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Simone Immler
- Department of Evolutionary Biology; Uppsala University; Uppsala Sweden
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Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete. PLoS Genet 2016; 12:e1006110. [PMID: 27327578 PMCID: PMC4915694 DOI: 10.1371/journal.pgen.1006110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/16/2016] [Indexed: 11/19/2022] Open
Abstract
In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system. Some fungi are capable of sexual reproduction without the need for a sexually compatible partner, a behavior called homothallism. For some of these fungi, it was observed that they carried in a single individual all the genes normally determining sexual identity in two distinct sexually compatible individuals, but in most cases the role of these genes is still unclear. Here we examined in detail the homothallic sexual cycle of the yeast Phaffia rhodozyma that belongs to the Basidiomycota, which is the fungal lineage that also includes the mushrooms. Phaffia rhodozyma produces astaxanthin, a pigment with antioxidant properties used in the food and cosmetic industries and is accessible to genetic modifications, so far aimed mainly at improving astaxanthin production. Here we harnessed these genetic tools to dissect the self-fertile life cycle of this yeast and found that all genes normally involved in two-partner sexual reproduction are also required for self-fertile sex in P. rhodozyma and propose a model describing molecular interactions required to trigger sexual development. We also generated preferably outcrossing strains, which are potentially useful for further improvement of P. rhodozyma as an industrial organism.
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Idnurm A, Hood ME, Johannesson H, Giraud T. Contrasted patterns in mating-type chromosomes in fungi: hotspots versus coldspots of recombination. FUNGAL BIOL REV 2015; 29:220-229. [PMID: 26688691 PMCID: PMC4680991 DOI: 10.1016/j.fbr.2015.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is striking that, while central to sexual reproduction, the genomic regions determining sex or mating-types are often characterized by suppressed recombination that leads to a decrease in the efficiency of selection, shelters genetic load, and inevitably contributes to their genic degeneration. Research on model and lesser-explored fungi has revealed similarities in recombination suppression of the genomic regions involved in mating compatibility across eukaryotes, but fungi also provide opposite examples of enhanced recombination in the genomic regions that determine their mating types. These contrasted patterns of genetic recombination (sensu lato, including gene conversion and ectopic recombination) in regions of the genome involved in mating compatibility point to important yet complex processes occurring in their evolution. A number of pieces in this puzzle remain to be solved, in particular on the unclear selective forces that may cause the patterns of recombination, prompting theoretical developments and experimental studies. This review thus points to fungi as a fascinating group for studying the various evolutionary forces at play in the genomic regions involved in mating compatibility.
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Affiliation(s)
- Alexander Idnurm
- School of BioSciences, University of Melbourne, VIC 3010, Australia
| | - Michael E. Hood
- Department of Biology, Amherst College, Amherst, Massachusetts 01002 USA
| | - Hanna Johannesson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution, UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360, Université Paris-Sud, 91405 Orsay cedex, France
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46
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James TY. Why mushrooms have evolved to be so promiscuous: Insights from evolutionary and ecological patterns. FUNGAL BIOL REV 2015. [DOI: 10.1016/j.fbr.2015.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Hood ME, Scott M, Hwang M. Breaking linkage between mating compatibility factors: Tetrapolarity in Microbotryum. Evolution 2015; 69:2561-72. [PMID: 26339889 DOI: 10.1111/evo.12765] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/02/2015] [Indexed: 12/31/2022]
Abstract
Linkage of genes determining separate self-incompatibility mechanisms is a general expectation of sexual eukaryotes that helps to resolve conflicts between reproductive assurance and recombination. However, in some organisms, multiple loci are required to be heterozygous in offspring while segregating independently in meiosis. This condition, termed "tetrapolarity" in basidiomycete fungi, originated in the ancestor to that phylum, and there have been multiple reports of subsequent transitions to "bipolarity" (i.e., linkage of separate mating factors). In the genus Microbotryum, we present the first report of the breaking of linkage between two haploid self-incompatibility factors and derivation of a tetrapolar breeding system. This breaking of linkage is associated with major alteration of genome structure, with the compatibility factors residing on separate mating-type chromosome pairs, reduced in size but retaining the structural dimorphism characteristic for regions of recombination suppression. The challenge to reproductive assurance from unlinked compatibility factors may be overcome by the automictic mating system in Microbotryum (i.e., mating among products of the same meiosis). As a curious outcome, this linkage transition and its effects upon outcrossing compatibility rates may reinforce automixis as a mating system. These observations contribute to understanding mating systems and linkage as fundamental principles of sexual life cycles, with potential impacts on conventional wisdom regarding mating-type evolution.
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Affiliation(s)
- Michael E Hood
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002.
| | - Molly Scott
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002
| | - Mindy Hwang
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002
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Evolution of Mating Systems in Basidiomycetes and the Genetic Architecture Underlying Mating-Type Determination in the Yeast Leucosporidium scottii. Genetics 2015; 201:75-89. [PMID: 26178967 DOI: 10.1534/genetics.115.177717] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/13/2015] [Indexed: 11/18/2022] Open
Abstract
In most fungi, sexual reproduction is bipolar; that is, two alternate sets of genes at a single mating-type (MAT) locus determine two mating types. However, in the Basidiomycota, a unique (tetrapolar) reproductive system emerged in which sexual identity is governed by two unlinked MAT loci, each of which controls independent mechanisms of self/nonself recognition. Tetrapolar-to-bipolar transitions have occurred on multiple occasions in the Basidiomycota, resulting, for example, from linkage of the two MAT loci into a single inheritable unit. Nevertheless, owing to the scarcity of molecular data regarding tetrapolar systems in the earliest-branching lineage of the Basidiomycota (subphylum Pucciniomycotina), it is presently unclear if the last common ancestor was tetrapolar or bipolar. Here, we address this question, by investigating the mating system of the Pucciniomycotina yeast Leucosporidium scottii. Using whole-genome sequencing and chromoblot analysis, we discovered that sexual reproduction is governed by two physically unlinked gene clusters: a multiallelic homeodomain (HD) locus and a pheromone/receptor (P/R) locus that is biallelic, thereby dismissing the existence of a third P/R allele as proposed earlier. Allele distribution of both MAT genes in natural populations showed that the two loci were in strong linkage disequilibrium, but independent assortment of MAT alleles was observed in the meiotic progeny of a test cross. The sexual cycle produces fertile progeny with similar proportions of the four mating types, but approximately 2/3 of the progeny was found to be nonhaploid. Our study adds to others in reinforcing tetrapolarity as the ancestral state of all basidiomycetes.
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Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. Genetics 2015; 200:1275-84. [PMID: 26044594 PMCID: PMC4574255 DOI: 10.1534/genetics.115.177709] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/02/2015] [Indexed: 12/02/2022] Open
Abstract
Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recombination often are enriched in transposable elements and therefore can be challenging to assemble. Here we show that the latest improvements of the PacBio sequencing yield assembly of the whole genome of the anther-smut fungus, Microbotryum lychnidis-dioicae (the pathogenic fungus causing anther-smut disease of Silene latifolia), into finished chromosomes or chromosome arms, even for the repeat-rich mating-type chromosomes and centromeres. Suppressed recombination of the mating-type chromosomes is revealed to span nearly 90% of their lengths, with extreme levels of rearrangements, transposable element accumulation, and differentiation between the two mating types. We observed no correlation between allelic divergence and physical position in the nonrecombining regions of the mating-type chromosomes. This may result from gene conversion or from rearrangements of ancient evolutionary strata, i.e., successive steps of suppressed recombination. Centromeres were found to be composed mainly of copia-like transposable elements and to possess specific minisatellite repeats identical between the different chromosomes. We also identified subtelomeric motifs. In addition, extensive signs of degeneration were detected in the nonrecombining regions in the form of transposable element accumulation and of hundreds of gene losses on each mating-type chromosome. Furthermore, our study highlights the potential of the latest breakthrough PacBio chemistry to resolve complex genome architectures.
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Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh SS, Cuomo CA, Perlin MH, Gladieux P, Giraud T. Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi. Mol Biol Evol 2015; 32:928-43. [PMID: 25534033 PMCID: PMC4379399 DOI: 10.1093/molbev/msu396] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Dimorphic mating-type chromosomes in fungi are excellent models for understanding the genomic consequences of recombination suppression. Their suppressed recombination and reduced effective population size are expected to limit the efficacy of natural selection, leading to genomic degeneration. Our aim was to identify the sequences of the mating-type chromosomes (a1 and a2) of the anther-smut fungi and to investigate degeneration in their nonrecombining regions. We used the haploid a1 Microbotryum lychnidis-dioicae reference genome sequence. The a1 and a2 mating-type chromosomes were both isolated electrophoretically and sequenced. Integration with restriction-digest optical maps identified regions of recombination and nonrecombination in the mating-type chromosomes. Genome sequence data were also obtained for 12 other Microbotryum species. We found strong evidence of degeneration across the genus in the nonrecombining regions of the mating-type chromosomes, with significantly higher rates of nonsynonymous substitution (dN/dS) than in nonmating-type chromosomes or in recombining regions of the mating-type chromosomes. The nonrecombining regions of the mating-type chromosomes also showed high transposable element content, weak gene expression, and gene losses. The levels of degeneration did not differ between the a1 and a2 mating-type chromosomes, consistent with the lack of homogametic/heterogametic asymmetry between them, and contrasting with X/Y or Z/W sex chromosomes.
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Affiliation(s)
- Eric Fontanillas
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France
| | | | - Hélène Badouin
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France
| | - Elsa Petit
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France Department of Biology, Amherst College
| | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Jérôme Gouzy
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Damien M de Vienne
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gabriela Aguileta
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France CNRS UMR 8030, Evry, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Su San Toh
- Department of Biology, Program on Disease Evolution, University of Louisville
| | | | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville
| | - Pierre Gladieux
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France
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