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Ryu JS, Park B, van Peer AF, Na KS, Lee SH. Quantitative trait loci analysis for molecular markers linked to agricultural traits of Pleurotus ostreatus. PLoS One 2024; 19:e0308832. [PMID: 39133731 PMCID: PMC11318876 DOI: 10.1371/journal.pone.0308832] [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: 02/04/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Pleurotus ostreatus is a global mushroom crop with nutritional and medicinal benefits. However, the genetic basis of several commercial traits remains unknown. To address this, we analyzed the quantitative trait loci (QTLs) for two representative cultivars, "Heuktari" and "Miso," with apparently distinct alleles. A genetic map with 11 linkage groups was constructed, in which 27 QTLs were assigned to 14 traits. The explained phenotypic variations in QTLs ranged from 7.8% to 22.0%. Relatively high LOD values of 6.190 and 5.485 were estimated for the pinheading period and the number of valid stipes, respectively. Some QTL-derived molecular markers showed potential enhancement rates of selection precision in inbred lines, especially for cap shape (50%) and cap thickness (30%). Candidate genes were inferred from the QTL regions and validated using qRT-PCR, particularly for the cysteine and glutathione pathway, in relation to cap yellowness. The molecular markers in this study are expected to facilitate the breeding of the Heuktari and Miso lines and provide probes to identify related genes in P. ostreatus.
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Affiliation(s)
- Jae-San Ryu
- Department of Mushroom Science, Korea National University of Agriculture and Fisheries, Jeonju, Jeonju-si, Jeollabuk-do, South Korea
| | - Bokyung Park
- Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Arend F. van Peer
- Plant Breeding, Wageningen University and Research, PB Wageningen, The Netherlands
| | - Kyeong Sook Na
- Department of Mushroom Science, Korea National University of Agriculture and Fisheries, Jeonju, Jeonju-si, Jeollabuk-do, South Korea
| | - Song Hee Lee
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea
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Nakazawa T, Kawauchi M, Otsuka Y, Han J, Koshi D, Schiphof K, Ramírez L, Pisabarro AG, Honda Y. Pleurotus ostreatus as a model mushroom in genetics, cell biology, and material sciences. Appl Microbiol Biotechnol 2024; 108:217. [PMID: 38372792 PMCID: PMC10876731 DOI: 10.1007/s00253-024-13034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
Pleurotus ostreatus, also known as the oyster mushroom, is a popular edible mushroom cultivated worldwide. This review aims to survey recent progress in the molecular genetics of this fungus and demonstrate its potential as a model mushroom for future research. The development of modern molecular genetic techniques and genome sequencing technologies has resulted in breakthroughs in mushroom science. With efficient transformation protocols and multiple selection markers, a powerful toolbox, including techniques such as gene knockout and genome editing, has been developed, and numerous new findings are accumulating in P. ostreatus. These include molecular mechanisms of wood component degradation, sexual development, protein secretion systems, and cell wall structure. Furthermore, these techniques enable the identification of new horizons in enzymology, biochemistry, cell biology, and material science through protein engineering, fluorescence microscopy, and molecular breeding. KEY POINTS: • Various genetic techniques are available in Pleurotus ostreatus. • P. ostreatus can be used as an alternative model mushroom in genetic analyses. • New frontiers in mushroom science are being developed using the fungus.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yuitsu Otsuka
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junxian Han
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daishiro Koshi
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Kim Schiphof
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006, Pamplona, Spain
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
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3
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Vreeburg SME, Auxier B, Jacobs B, Bourke PM, van den Heuvel J, Zwaan BJ, Aanen DK. A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus. BMC Genomics 2023; 24:123. [PMID: 36927388 PMCID: PMC10021994 DOI: 10.1186/s12864-023-09210-x] [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: 06/29/2021] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The termite-fungus symbiosis is an ancient stable mutualism of two partners that reproduce and disperse independently. With the founding of each termite colony the symbiotic association must be re-established with a new fungus partner. Complementarity in the ability to break down plant substrate may help to stabilize this symbiosis despite horizontal symbiont transmission. An alternative, non-exclusive, hypothesis is that a reduced rate of evolution may contribute to stabilize the symbiosis, the so-called Red King Effect. METHODS To explore this concept, we produced the first linkage map of a species of Termitomyces, using genotyping by sequencing (GBS) of 88 homokaryotic offspring. We constructed a highly contiguous genome assembly using PacBio data and a de-novo evidence-based annotation. This improved genome assembly and linkage map allowed for examination of the recombination landscape and its potential effect on the mutualistic lifestyle. RESULTS Our linkage map resulted in a genome-wide recombination rate of 22 cM/Mb, lower than that of other related fungi. However, the total map length of 1370 cM was similar to that of other related fungi. CONCLUSIONS The apparently decreased rate of recombination is primarily due to genome expansion of islands of gene-poor repetitive sequences. This study highlights the importance of inclusion of genomic context in cross-species comparisons of recombination rate.
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Affiliation(s)
- Sabine M E Vreeburg
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Ben Auxier
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands.
| | - Bas Jacobs
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands.,Biometris, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, the Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
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4
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Analysis of Biochemical and Genetic Variability of Pleurotus ostreatus Based on the β-Glucans and CDDP Markers. J Fungi (Basel) 2022; 8:jof8060563. [PMID: 35736046 PMCID: PMC9225165 DOI: 10.3390/jof8060563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Oyster mushroom (Pleurotus ostreatus) is still one of the most cultivated edible and medicinal mushrooms. Despite its frequent cultivation around the world, there is currently just a little information available on the variability of strains in terms of the content of β-glucans in them. This work presents an extensive study of 60 strains in terms of the content of α-glucans and β-glucans in their caps and stipes. The authenticity of the production strains based on an analysis of the variability of their genome by CDDP (Conserved DNA-derived polymorphism) markers was confirmed, whereas identical CDDP profiles were identified between samples 45, 89, 95, and 96. Genetic variability of the analyzed production strains showed a high polymorphism and effective discriminative power of the used marking technique. Medium positive correlations were found among the CDDP profiles and β-glucan content in the group of strains that generated the same CDDP profiles, and low negative correlation was found among these profiles in the group of low β-glucan content strains. For the determination of glucans content, Mushroom and Yeast analytical enzymatic kit (Megazyme, Bray, Co. Wicklow, Ireland) were used. The results clearly showed that the stipe contains on average 33% more β-glucans than the cap. The minimum detected β-glucan content in the stipe was in strain no. 72, specifically 22%, and the maximum in strain no. 43, specifically 56%, which after the conversion represents a difference of 155%. From the point of view of β-glucan content, the stated strain no. 43 appears to be very suitable for the commercial production of β-glucans under certain conditions.
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Vogan AA, Martinossi-Allibert I, Ament-Velásquez SL, Svedberg J, Johannesson H. The spore killers, fungal meiotic driver elements. Mycologia 2022; 114:1-23. [PMID: 35138994 DOI: 10.1080/00275514.2021.1994815] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
During meiosis, both alleles of any given gene should have equal chances of being inherited by the progeny. There are a number of reasons why, however, this is not the case, with one of the most intriguing instances presenting itself as the phenomenon of meiotic drive. Genes that are capable of driving can manipulate the ratio of alleles among viable meiotic products so that they are inherited in more than half of them. In many cases, this effect is achieved by direct antagonistic interactions, where the driving allele inhibits or otherwise eliminates the alternative allele. In ascomycete fungi, meiotic products are packaged directly into ascospores; thus, the effect of meiotic drive has been given the nefarious moniker, "spore killing." In recent years, many of the known spore killers have been elevated from mysterious phenotypes to well-described systems at genetic, genomic, and molecular levels. In this review, we describe the known diversity of spore killers and synthesize the varied pieces of data from each system into broader trends regarding genome architecture, mechanisms of resistance, the role of transposable elements, their effect on population dynamics, speciation and gene flow, and finally how they may be developed as synthetic drivers. We propose that spore killing is common, but that it is under-observed because of a lack of studies on natural populations. We encourage researchers to seek new spore killers to build on the knowledge that these remarkable genetic elements can teach us about meiotic drive, genomic conflict, and evolution more broadly.
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Affiliation(s)
- Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden.,Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 33077, Bordeaux CEDEX, France
| | - S Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Jesper Svedberg
- Department of Biomolecular Engineering, University of California, -Santa Cruz, Santa Cruz, California 95064
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
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6
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Oh YL, Choi IG, Jang KY, Kim MS, Oh MJ, Im JH. SNP-Based Genetic Linkage Map and Quantitative Trait Locus Mapping Associated with the Agronomically Important Traits of Hypsizygus marmoreus. MYCOBIOLOGY 2021; 49:589-598. [PMID: 35035250 PMCID: PMC8725901 DOI: 10.1080/12298093.2021.2018784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18 × KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value ≤ .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value ≤ .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus.
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Affiliation(s)
- Youn-Lee Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Korea
| | - Kab-Yeul Jang
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Min-Seek Kim
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Min ji Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Ji-Hoon Im
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
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7
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Pérez G, Lopez-Moya F, Chuina E, Ibañez-Vea M, Garde E, López-Llorca LV, Pisabarro AG, Ramírez L. Strain Degeneration in Pleurotus ostreatus: A Genotype Dependent Oxidative Stress Process Which Triggers Oxidative Stress, Cellular Detoxifying and Cell Wall Reshaping Genes. J Fungi (Basel) 2021; 7:jof7100862. [PMID: 34682283 PMCID: PMC8537115 DOI: 10.3390/jof7100862] [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: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/13/2022] Open
Abstract
Strain degeneration has been defined as a decrease or loss in the yield of important commercial traits resulting from subsequent culture, which ultimately leads to Reactive Oxygen Species (ROS) production. Pleurotus ostreatus is a lignin-producing nematophagous edible mushroom. Mycelia for mushroom production are usually maintained in subsequent culture in solid media and frequently show symptoms of strain degeneration. The dikaryotic strain P. ostreatus (DkN001) has been used in our lab as a model organism for different purposes. Hence, different tools have been developed to uncover genetic and molecular aspects of this fungus. In this work, strain degeneration was studied in a full-sib monokaryotic progeny of the DkN001 strain with fast (F) and slow (S) growth rates by using different experimental approaches (light microscopy, malondialdehyde levels, whole-genome transcriptome analysis, and chitosan effect on monokaryotic mycelia). The results obtained showed that: (i) strain degeneration in P. ostreatus is linked to oxidative stress, (ii) the oxidative stress response in monokaryons is genotype dependent, (iii) stress and detoxifying genes are highly expressed in S monokaryons with symptoms of strain degeneration, (iv) chitosan addition to F and S monokaryons uncovered the constitutive expression of both oxidative stress and cellular detoxifying genes in S monokaryon strains which suggest their adaptation to oxidative stress, and (v) the overexpression of the cell wall genes, Uap1 and Cda1, in S monokaryons with strain degeneration phenotype indicates cell wall reshaping and the activation of High Osmolarity Glycerol (HOG) and Cell Wall Integrity (CWI) pathways. These results could constitute a hallmark for mushroom producers to distinguish strain degeneration in commercial mushrooms.
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Affiliation(s)
- Gumer Pérez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Federico Lopez-Moya
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Emilia Chuina
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - María Ibañez-Vea
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Edurne Garde
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Luis V. López-Llorca
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Antonio G. Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
- Correspondence:
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8
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Genetic Linkage and Physical Mapping for an Oyster Mushroom ( Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color. Appl Environ Microbiol 2021; 87:e0095321. [PMID: 34406836 DOI: 10.1128/aem.00953-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.
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9
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Vidal-Diez de Ulzurrun G, Lee YY, Stajich JE, Schwarz EM, Hsueh YP. Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains. G3 (BETHESDA, MD.) 2021; 11:jkaa007. [PMID: 33585863 PMCID: PMC8022975 DOI: 10.1093/g3journal/jkaa007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/14/2020] [Indexed: 11/14/2022]
Abstract
Pleurotus mushrooms are among the most cultivated fungi in the world and are highly valuable for food, medicine, and biotechnology industries. Furthermore, Pleurotus species are carnivorous fungi; they can rapidly paralyze and kill nematodes when nutrient-deprived. The predator-prey interactions between Pleurotus and nematodes are still widely unexplored. Moreover, the molecular mechanisms and the genes involved in the carnivorous behavior of Pleurotus mushrooms remain a mystery. We are attempting to understand the interactions between Pleurotus mushrooms and their nematode prey through genetic and genomic analyses. Two single spores (ss2 and ss5) isolated from a fruiting body of Pleurotus pulmonarius exhibited significant differences in growth and toxicity against nematodes. Thus, using PacBio long reads, we assembled and annotated two high-quality genomes for these two isolates of P. pulmonarius. Each of these assemblies contains 23 scaffolds, including 6 (ss2) and 8 (ss5) telomere-to-telomere scaffolds, and they are among the most complete assembled genomes of the Pleurotus species. Comparative analyses identified the genomic differences between the two P. pulmonarius strains. In sum, this work provides a genomic resource that will be invaluable for better understanding the Italian oyster mushroom P. pulmonarius.
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Affiliation(s)
| | - Yi-Yun Lee
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Ave. Riverside, CA 92521, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology 351, 526 Campus Road, Ithaca, NY 14853-2703, USA
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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10
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Yoneyama S, Maeda K, Sadamori A, Saitoh S, Tsuda M, Azuma T, Nagano A, Tomiyama T, Matsumoto T. Construction of a genetic linkage map and detection of quantitative trait locus for the ergothioneine content in tamogitake mushroom ( Pleurotus cornucopiae var. citrinopileatus). MYCOSCIENCE 2021; 62:71-80. [PMID: 37090022 PMCID: PMC9157747 DOI: 10.47371/mycosci.2020.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 11/16/2022]
Abstract
Developing high-content strains of L-ergothioneine (EGT), an antioxidant amino acid, is an important breeding target for tamogitake mushroom, Pleurotus cornucopiae var. citrinopileatus. We constructed a genetic linkage map based on segregation analysis of markers in 105 F1 progenies. The loci of 245 markers, including 10 AFLP markers, 195 Rad markers, 2 mating type factors, and 38 gene markers, were mapped. The map contained 12 linkage groups with a total genetic distance of 906.8 cM, and an average marker interval of 4.0 cM. The population from crossing between tester monokaryon and F1 progenies was used to characterize quantitative trait loci (QTL) for EGT content. With composite interval mapping (CIM) method, QTL of EGT content were found to be located in linkage group 10, having a Logarithm of the odds (LOD) score of 2.53 with a 10.1% contribution rate. Moreover, a single nucleotide polymorphism (SNP), A/T, was identified in a gene region of the genome in the neighborhood where the QTL peak existed. This SNP genotype was in good agreement with the EGT phenotypes of each strain in the both QTL population and wild population. Thus, this SNP would have great potential value to use the marker-assisted selection (MAS) for this mushroom with high EGT content.
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Affiliation(s)
- Shozo Yoneyama
- Forest Products Research Institute, Hokkaido Research Organization
| | - Kaede Maeda
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
| | - Ayuka Sadamori
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
| | - Sayaka Saitoh
- Forest Products Research Institute, Hokkaido Research Organization
| | - Mayumi Tsuda
- Forest Products Research Institute, Hokkaido Research Organization
| | - Tomonori Azuma
- Forest Products Research Institute, Hokkaido Research Organization
| | | | | | - Teruyuki Matsumoto
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
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Gong W, Xie C, Zhou Y, Zhu Z, Wang Y, Peng Y. A Resequencing-Based Ultradense Genetic Map of Hericium erinaceus for Anchoring Genome Sequences and Identifying Genetic Loci Associated With Monokaryon Growth. Front Microbiol 2020; 10:3129. [PMID: 32082271 PMCID: PMC7005679 DOI: 10.3389/fmicb.2019.03129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
Hericium erinaceus has attracted tremendous interest owing to its compelling health-promoting properties. However, breeding of elite cultivars of H. erinaceus is hindered by the lack of a genetic and molecular toolbox. Here, we performed resequencing analysis of 127 F1 single-spore isolates and constructed the first high-resolution genetic map of H. erinaceus. With the use of recombination bins as markers, an ultradense genetic map consisting of 1,174 bins (including 37,082 single-nucleotide polymorphisms) was generated. This newly developed genetic map covered 1,096.5 cM, with an average bin spacing of 0.95 cM. High collinearity between genetic map and H. erinaceus genome assembly was revealed by aligning scaffolds to this genetic map using bin markers as anchors. The application of this newly developed genetic map in quantitative trait locus (QTL) mapping was also elucidated, and four QTLs for monokaryon growth were recovered. One QTL, mgr1, which contributes 12.1% of growth variations, was located near the mating type A (MAT-A) loci. Overall, this newly constructed high-resolution genetic map (or bin map) could be used as reference in future genetic, genomic, and breeding studies on H. erinaceus.
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Affiliation(s)
| | | | | | | | | | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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12
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Gupta DK, Rühl M, Mishra B, Kleofas V, Hofrichter M, Herzog R, Pecyna MJ, Sharma R, Kellner H, Hennicke F, Thines M. The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. BMC Genomics 2018; 19:48. [PMID: 29334897 PMCID: PMC5769442 DOI: 10.1186/s12864-017-4430-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. CONCLUSIONS The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
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Affiliation(s)
- Deepak K Gupta
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.,Project Group "Bioresources", Fraunhofer IME, Giessen, Germany
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Vanessa Kleofas
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Martin Hofrichter
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Robert Herzog
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Marek J Pecyna
- University of Applied Sciences Zittau/Görlitz, Zittau, Germany
| | - Rahul Sharma
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany
| | - Harald Kellner
- International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Florian Hennicke
- Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany. .,Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands.
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. .,LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.
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13
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Gao W, Qu J, Zhang J, Sonnenberg A, Chen Q, Zhang Y, Huang C. A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci. BMC Genomics 2018; 19:18. [PMID: 29304732 PMCID: PMC5755439 DOI: 10.1186/s12864-017-4421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/27/2017] [Indexed: 11/21/2022] Open
Abstract
Background Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs. Results Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus. Conclusions This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4421-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Anton Sonnenberg
- Plant Breeding, Wageningen University & Research Centre, 6708, PB, Wageningen, The Netherlands
| | - Qiang Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Yan Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China. .,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
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14
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Construction of a genetic linkage map and QTL mapping of agronomic traits in Auricularia auricula-judae. J Microbiol 2017; 55:792-799. [PMID: 28956350 DOI: 10.1007/s12275-017-7241-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/07/2017] [Accepted: 08/20/2017] [Indexed: 10/18/2022]
Abstract
Auricularia auricula-judae is a traditional edible fungus that is cultivated widely in China. In this study, a genetic linkage map for A. auricula-judae was constructed using a mapping population consisting of 138 monokaryons derived from a hybrid strain (A119-5). The monokaryotic parent strains A14-5 and A18-119 were derived from two cultivated varieties, A14 (Qihei No. 1) and A18 (Qihei No. 2), respectively. In total, 130 simple sequence repeat markers were mapped. These markers were developed using the whole genome sequence of A. auricula-judae and amplified in A14-5, A18- 119, and the mapping population. The map consisted of 11 linkage groups (LGs) spanning 854 cM, with an average interval length of 6.57 cM. A testcross population was derived from crossing between the monokaryon A184-57 (from the wild strain A184 as a tester strain) and the mapping population. Important agronomic trait-related QTLs, including mycelium growth rate on potato dextrose agar for the mapping population, mycelium growth rate on potato dextrose agar and sawdust for the testcross population, growth period (days from inoculation to fruiting body harvesting), and yield for the testcross population, were identified using the composite interval mapping method. Six mycelium growth raterelated QTLs were identified on LG1 and LG4, two growth period-related QTLs were identified on LG2, and three yieldrelated QTLs were identified on LG2 and LG6. The results showed no linkage relationship between mycelium growth rate and growth period. The present study provides a foundation for locating genes for important agronomic characteristics in A. auricula-judae in the future.
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15
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Borgognone A, Castanera R, Muguerza E, Pisabarro AG, Ramírez L. Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus. DNA Res 2017; 24:103-115. [PMID: 28431016 PMCID: PMC5397611 DOI: 10.1093/dnares/dsw060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/14/2016] [Indexed: 01/31/2023] Open
Abstract
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.
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Affiliation(s)
| | | | | | | | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
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16
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Peñas MM, Aranguren J, Ramírez L, Pisabarro AG. Structure of gene coding for the fruit body-specific hydrophobin Fbh1 of the edible basidiomycetePleurotus ostreatus. Mycologia 2017; 96:75-82. [DOI: 10.1080/15572536.2005.11832999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Antonio G. Pisabarro
- Departamento de Producción Agraria, Universidad Pública de Navarra, E-31006 Pamplona, Spain
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17
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James TY, Sun S, Li W, Heitman J, Kuo HC, Lee YH, Asiegbu FO, Olson Å. Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Mycologia 2017; 105:1374-90. [DOI: 10.3852/13-162] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | | | | | | | - Åke Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, S-75007 Uppsala, Sweden
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18
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Detection of Edible Mushroom Species by Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Alfaro M, Castanera R, Lavín JL, Grigoriev IV, Oguiza JA, Ramírez L, Pisabarro AG. Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungusPleurotus ostreatus. Environ Microbiol 2016; 18:4710-4726. [DOI: 10.1111/1462-2920.13360] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Alfaro
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Raúl Castanera
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - José L. Lavín
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park; Derio 48160 Spain
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - José A. Oguiza
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Lucía Ramírez
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Antonio G. Pisabarro
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
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20
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Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii. Fungal Genet Biol 2016; 92:50-64. [PMID: 27166667 DOI: 10.1016/j.fgb.2016.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/27/2016] [Accepted: 05/07/2016] [Indexed: 01/01/2023]
Abstract
Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes.
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21
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Foulongne-Oriol M, Rocha de Brito M, Cabannes D, Clément A, Spataro C, Moinard M, Dias ES, Callac P, Savoie JM. The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus. G3 (BETHESDA, MD.) 2016; 6:1217-26. [PMID: 26921302 PMCID: PMC4856074 DOI: 10.1534/g3.115.025718] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/21/2016] [Indexed: 01/15/2023]
Abstract
Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens.
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Affiliation(s)
| | - Manuela Rocha de Brito
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France Departamento de Biologia, UFLA, Universidade Federal de Lavras, C.P. 3037, 37200-000, Lavras, MG, Brazil
| | - Delphine Cabannes
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
| | - Aurélien Clément
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
| | - Cathy Spataro
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
| | - Magalie Moinard
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
| | - Eustáquio Souza Dias
- Departamento de Biologia, UFLA, Universidade Federal de Lavras, C.P. 3037, 37200-000, Lavras, MG, Brazil
| | - Philippe Callac
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
| | - Jean-Michel Savoie
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, Villenave d'Ornon, France
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22
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Qu J, Huang C, Zhang J. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene 2016; 575:524-530. [DOI: 10.1016/j.gene.2015.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022]
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23
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Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map. Int J Mol Sci 2015. [PMID: 26204838 PMCID: PMC4519972 DOI: 10.3390/ijms160716669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.
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24
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Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M, Gabaldón T, Pisabarro AG, Oguiza JA, Ramírez L. Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics 2014; 15:1071. [PMID: 25480150 PMCID: PMC4289320 DOI: 10.1186/1471-2164-15-1071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species. RESULTS Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons. CONCLUSION P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lucía Ramírez
- Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain.
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25
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Pernaci M, De Mita S, Andrieux A, Pétrowski J, Halkett F, Duplessis S, Frey P. Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. FRONTIERS IN PLANT SCIENCE 2014; 5:454. [PMID: 25309554 PMCID: PMC4159982 DOI: 10.3389/fpls.2014.00454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 08/21/2014] [Indexed: 05/16/2023]
Abstract
The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.
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Affiliation(s)
- Michaël Pernaci
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Stéphane De Mita
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Axelle Andrieux
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Jérémy Pétrowski
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Fabien Halkett
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Pascal Frey
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
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Gong WB, Liu W, Lu YY, Bian YB, Zhou Y, Kwan HS, Cheung MK, Xiao Y. Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes. Fungal Biol 2014; 118:295-308. [PMID: 24607353 DOI: 10.1016/j.funbio.2014.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 12/01/2022]
Abstract
The most saturated linkage map for Lentinula edodes to date was constructed based on a monokaryotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion-deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07 %-23.71 % of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes.
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Affiliation(s)
- Wen-Bing Gong
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, Hubei Province, PR China; Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China
| | - Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China; Institute of Hydrobiology, Chinese Academy of Sciences, Hubei Province 430072, PR China
| | - Ying-Ying Lu
- Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China; Institute of Crop Genetic Resource, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou Province, PR China
| | - Yin-Bing Bian
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, Hubei Province, PR China; Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China
| | - Yan Zhou
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, Hubei Province, PR China; Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China
| | - Yang Xiao
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture), Huazhong Agricultural University, Wuhan 430070, Hubei Province, PR China; Institute of Applied Mycology, Huazhong Agricultural University, Hubei Province 430070, PR China.
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Castanera R, Omarini A, Santoyo F, Pérez G, Pisabarro AG, Ramírez L. Non-additive transcriptional profiles underlie dikaryotic superiority in Pleurotus ostreatus laccase activity. PLoS One 2013; 8:e73282. [PMID: 24039902 PMCID: PMC3764117 DOI: 10.1371/journal.pone.0073282] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 07/18/2013] [Indexed: 12/04/2022] Open
Abstract
Background The basidiomycete Pleurotus ostreatus is an efficient producer of laccases, a group of enzymes appreciated for their use in multiple industrial processes. The aim of this study was to reveal the molecular basis of the superiority of laccase production by dikaryotic strains compared to their parental monokaryons. Methodology/Principal Findings We bred and studied a set of dikaryotic strains starting from a meiotic population of monokaryons. We then completely characterised the laccase allelic composition, the laccase gene expression and activity profiles in the dikaryotic strain N001, in two of its meiotic full-sib monokaryons and in the dikaryon formed from their mating. Conclusions/Significance Our results suggested that the dikaryotic superiority observed in laccase activity was due to non-additive transcriptional increases in lacc6 and lacc10 genes. Furthermore, the expression of these genes was divergent in glucose- vs. lignocellulose-supplemented media and was highly correlated to the detected extracellular laccase activity. Moreover, the expression profile of lacc2 in the dikaryotic strains was affected by its allelic composition, indicating a putative single locus heterozygous advantage.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Alejandra Omarini
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Francisco Santoyo
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Gúmer Pérez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Antonio G. Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
- * E-mail:
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Parenti A, Muguerza E, Iroz AR, Omarini A, Conde E, Alfaro M, Castanera R, Santoyo F, Ramírez L, Pisabarro AG. Induction of laccase activity in the white rot fungus Pleurotus ostreatus using water polluted with wheat straw extracts. BIORESOURCE TECHNOLOGY 2013; 133:142-9. [PMID: 23425584 DOI: 10.1016/j.biortech.2013.01.072] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/11/2013] [Accepted: 01/13/2013] [Indexed: 05/06/2023]
Abstract
The purpose of this work was to explore the use of polluted water effluents from wheat straw using industries as inducers of lignocellulolytic enzymatic activities in cultures of white rot basidiomycetes. For this purpose, we studied the effect of a wheat straw water extract on the evolution of the laccase activity recovered from submerged cultures of Pleurotus ostreatus made in different media and under various culture conditions. Our results demonstrated an accumulative induction effect in all the cultures and conditions tested. This induction is parallel to changes in the laccase electrophoretic profiles recovered from the culture supernatants. The isoenzyme that appeared to be mainly responsible for the laccase activity under these conditions was laccase 10, as confirmed by sequencing the induced protein. These results support the idea of using wheat straw effluents as inducers in liquid cultures of P. ostreatus mycelia for the production of ligninolytic enzymatic cocktails.
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Affiliation(s)
- Alejandra Parenti
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
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Molecular characterization of sexual diversity in a population of Serpula lacrymans, a tetrapolar basidiomycete. G3-GENES GENOMES GENETICS 2013; 3:145-52. [PMID: 23390592 PMCID: PMC3564976 DOI: 10.1534/g3.112.003731] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/25/2012] [Indexed: 12/22/2022]
Abstract
Different mating systems have evolved in the fungal kingdom, including a tetrapolar multiallelic mating system in many basidiomycetes. In tetrapolar species, the presence of different alleles at two mating loci (MAT A and MAT B) is necessary for mating to occur. The tetrapolar fungus Serpula lacrymans causes wood-decay in buildings in temperate regions worldwide and is present in Europe with a genetically homogeneous founder population. Using genome sequence data, we annotated the two mating type loci for S. lacrymans and found the expected synteny with other basidiomycetes, except for a retrotransposon being present in one locus (MAT A). We developed markers linked to the MAT A and MAT B regions and used these to investigate the mating type diversity in the European population. Moreover, we found a good match between the genetic markers and functional mating types as revealed by segregation and mating studies. A low diversity of mating types is present in the European S. lacrymans population caused by the founder event where a limited number of genotypes were introduced. This finding contrasts the situation in natural fungal populations where a high diversity of mating types is normally present. Although S. lacrymans has a large and viable population in Europe, we argue that the low mating type diversity restrains the dispersal and establishment of the fungus.
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Janusz G, Kucharzyk KH, Pawlik A, Staszczak M, Paszczynski AJ. Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression and regulation. Enzyme Microb Technol 2012. [PMID: 23199732 DOI: 10.1016/j.enzmictec.2012.10.003] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive research efforts have been dedicated to characterizing expression of laccases and peroxidases and their regulation in numerous fungal species. Much attention has been brought to these enzymes broad substrate specificity resulting in oxidation of a variety of organic compounds which brings about possibilities of their utilization in biotechnological and environmental applications. Research attempts have resulted in increased production of both laccases and peroxidases by the aid of heterologous and homologous expression. Through analysis of promoter regions, protein expression patterns and culture conditions manipulations it was possible to compare and identify common pathways of these enzymes' production and secretion. Although laccase and peroxidase proteins have been crystallized and thoroughly analyzed, there are still a lot of questions remaining about their evolutionary origin and the physiological functions. This review describes the present understanding of promoter sequences and correlation between the observed regulatory effects on laccase, manganese peroxidase and lignin peroxidase genes transcript levels and the presence of specific response elements.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland.
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Foulongne-Oriol M. Genetic linkage mapping in fungi: current state, applications, and future trends. Appl Microbiol Biotechnol 2012; 95:891-904. [PMID: 22743715 DOI: 10.1007/s00253-012-4228-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences.
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Assignment of RAPD marker probes designed from 12 linkage groups of Flammulina velutipes to CHEF-separated chromosomal DNAs. MYCOSCIENCE 2012. [DOI: 10.1007/s10267-011-0156-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sivolapova AB, Shnyreva AV, Sonnenberg A, Baars I. DNA marking of some quantitative trait loci in the cultivated edible mushroom Pleurotus ostreatus (Fr.) Kumm. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412040114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Transcriptional and enzymatic profiling of Pleurotus ostreatus laccase genes in submerged and solid-state fermentation cultures. Appl Environ Microbiol 2012; 78:4037-45. [PMID: 22467498 DOI: 10.1128/aem.07880-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the white rot basidiomycete Pleurotus ostreatus includes 12 phenol oxidase (laccase) genes. In this study, we examined their expression profiles in different fungal strains under different culture conditions (submerged and solid cultures) and in the presence of a wheat straw extract, which was used as an inducer of the laccase gene family. We used a reverse transcription-quantitative PCR (RT-qPCR)-based approach and focused on determining the reaction parameters (in particular, the reference gene set for the normalization and reaction efficiency determinations) used to achieve an accurate estimation of the relative gene expression values. The results suggested that (i) laccase gene transcription is upregulated in the induced submerged fermentation (iSmF) cultures but downregulated in the solid fermentation (SSF) cultures, (ii) the Lacc2 and Lacc10 genes are the main sources of laccase activity in the iSmF cultures upon induction with water-soluble wheat straw extracts, and (iii) an additional, as-yet-uncharacterized activity (Unk1) is specifically induced in SSF cultures that complements the activity of Lacc2 and Lacc10. Moreover, both the enzymatic laccase activities and the Lacc gene family transcription profiles greatly differ between closely related strains. These differences can be targeted for biotechnological breeding programs for enzyme production in submerged fermentation reactors.
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Construction of a genetic linkage map based on amplified fragment length polymorphism markers and development of sequence-tagged site markers for marker-assisted selection of the sporeless trait in the oyster mushroom (Pleurotus eryngii). Appl Environ Microbiol 2011; 78:1496-504. [PMID: 22210222 DOI: 10.1128/aem.07052-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Quél. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection.
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36
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Foulongne-Oriol M, Dufourcq R, Spataro C, Devesse C, Broly A, Rodier A, Savoie JM. Comparative linkage mapping in the white button mushroom Agaricus bisporus provides foundation for breeding management. Curr Genet 2010; 57:39-50. [DOI: 10.1007/s00294-010-0325-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 10/06/2010] [Accepted: 10/17/2010] [Indexed: 10/18/2022]
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Kubisiak TL, Anderson CL, Amerson HV, Smith JA, Davis JM, Nelson CD. A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme. Fungal Genet Biol 2010; 48:266-74. [PMID: 20888926 DOI: 10.1016/j.fgb.2010.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/24/2010] [Accepted: 09/27/2010] [Indexed: 11/30/2022]
Abstract
A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f.sp. fusiforme, the causal agent of fusiform rust disease in pines. DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10-5 were used to classify 10-5 seedling progeny as either resistant or susceptible. A single dikaryotic isolate (P2) heterozygous at the corresponding Avr1 gene was developed by crossing Fr1 avirulent isolate SC20-21 with Fr1 virulent isolate NC2-40. Bulk basidiospore inoculum derived from isolate P2 was used to challenge the pine progeny. The ability to unambiguously marker classify 10-5 progeny as resistant (selecting for virulence) or susceptible (non-selecting) permitted the genetic mapping of the corresponding Avr1 gene by bulked segregant analysis. Using this approach, 14 genetic markers significantly linked to Avr1 were identified and placed within the context of a genome-wide linkage map produced for isolate P2 using samples from susceptible seedlings.
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Affiliation(s)
- Thomas L Kubisiak
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, U.S. Department of Agriculture, 23332 Success Road, Saucier, MS 39574, USA.
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Foulongne-Oriol M, Spataro C, Cathalot V, Monllor S, Savoie JM. An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporusxA. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species. Fungal Genet Biol 2009; 47:226-36. [PMID: 20026415 DOI: 10.1016/j.fgb.2009.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 10/27/2009] [Accepted: 12/09/2009] [Indexed: 01/27/2023]
Abstract
A genetic linkage map for the edible basidiomycete Agaricus bisporus was constructed from 118 haploid homokaryons derived from an intervarietal A. bisporus var. bisporus x A. bisporus var. burnettii hybrid. Two hundred and thirty-one AFLP, 21 SSR, 68 CAPS markers together with the MAT, BSN, PPC1 loci and one allozyme locus (ADH) were evenly spread over 13 linkage groups corresponding to the chromosomes of A. bisporus. The map covers 1156cM, with an average marker spacing of 3.9cM and encompasses nearly the whole genome. The average number of crossovers per chromosome per individual is 0.86. Normal recombination over the entire genome occurs in the heterothallic variety, burnettii, contrary to the homothallic variety, bisporus, which showed adaptive genome-wide suppressed recombination. This first comprehensive genetic linkage map for A. bisporus provides foundations for quantitative trait analyses and breeding programme monitoring, as well as genome organisation studies.
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Affiliation(s)
- Marie Foulongne-Oriol
- Mycologie et Sécurité des Aliments, INRA, Centre de Recherche Bordeaux-Aquitaine, Villenave d'Ornon Cedex, France.
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Xu X, Roberts T, Barbara D, Harvey NG, Gao L, Sargent DJ. A genetic linkage map of Venturia inaequalis, the causal agent of apple scab. BMC Res Notes 2009; 2:163. [PMID: 19689797 PMCID: PMC2732633 DOI: 10.1186/1756-0500-2-163] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 08/18/2009] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Venturia inaequalis is an economically-important disease of apple causing annual epidemics of scab worldwide. The pathogen is a heterothallic ascomycete with an annual cycle of sexual reproduction on infected apple leaf litter, followed by several cycles of asexual reproduction during the apple growing season. Current disease control is achieved mainly through scheduled applications of fungicides. Genetic linkage maps are essential for studying genome structure and organisation, and are a valuable tool for identifying the location of genes controlling important traits of interest such as avirulence, host specificity and mating type in V. inaequalis. In this study, we performed a wide cross under in vitro conditions between an isolate of V. inaequalis from China and one from the UK to obtain a genetically diverse mapping population of ascospore progeny isolates and produced a map using AFLP and microsatellite (SSR) markers. FINDINGS Eighty-three progeny were obtained from the cross between isolates C0154 (China) x 01/213 (UK). The progeny was screened with 18 AFLP primer combinations and 31 SSRs, and scored for the mating type locus MAT. A linkage map was constructed consisting of 294 markers (283 AFLPs, ten SSRs and the MAT locus), spanning eleven linkage groups and with a total map length of 1106 cM. The length of individual linkage groups ranged from 30.4 cM (Vi-11) to 166 cM (Vi-1). The number of molecular markers per linkage group ranged from 7 on Vi-11 to 48 on Vi-3; the average distance between two loci within each group varied from 2.4 cM (Vi-4) to 7.5 cM (Vi-9). The maximum map length between two markers within a linkage group was 15.8 cM. The MAT locus was mapped to a small linkage group and was tightly linked to two AFLP markers. The map presented is over four times longer than the previously published map of V. inaequalis which had a total genetic distance of just 270 cM. CONCLUSION A genetic linkage map is an important tool for investigating the genetics of important traits in V. inaequalis such as virulence factors, aggressiveness and mating type. The linkage map presented here represents a significant improvement over currently published maps for studying genome structure and organisation, and for mapping genes of economic importance on the V. inaequalis genome.
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Affiliation(s)
- Xiangming Xu
- East Malling Research, New Road, East Malling, ME19 6BJ, UK
| | - Tony Roberts
- East Malling Research, New Road, East Malling, ME19 6BJ, UK
| | - Dez Barbara
- Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Nick G Harvey
- East Malling Research, New Road, East Malling, ME19 6BJ, UK
| | - Liqiang Gao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, PR China
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Okuda Y, Murakami S, Matsumoto T. A genetic linkage map of Pleurotus pulmonarius based on AFLP markers, and localization of the gene region for the sporeless mutation. Genome 2009; 52:438-46. [PMID: 19448724 DOI: 10.1139/g09-021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the cultivation of edible mushrooms, including Pleurotus pulmonarius (Fr.) Quel., the enormous number of spores produced by fruiting bodies can adversely affect mushroom growers' health, mushroom cultivation facilities, and the genetic diversity of natural populations. In this study, we constructed a primary genetic linkage map and identified the locus associated with the sporulation-deficient (sporeless) mutation of P. pulmonarius using 150 progeny isolates derived from a cross between sporeless and wild-type isolates. Based on the segregation of 300 AFLP markers, two mating-type factors, and the sporeless trait, a linkage map was generated consisting of 12 linkage groups. The map covered a total genetic distance of 971 cM, with an average marker interval of 5.2 cM. The gene region responsible for the sporeless mutation was located in linkage group II including 40 AFLP markers and the A mating-type factor locus. Of these markers, the nearest marker to the sporeless locus was located 1.4 cM away. Construction of this P. pulmonarius genetic linkage map and identification of markers that are closely linked to the sporeless locus will facilitate marker-assisted selective breeding of a sporeless strain with economically important traits.
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Affiliation(s)
- Yasuhito Okuda
- The University Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan
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van der Nest MA, Slippers B, Steenkamp ET, De Vos L, Van Zyl K, Stenlid J, Wingfield MJ, Wingfield BD. Genetic linkage map for Amylostereum areolatum reveals an association between vegetative growth and sexual and self-recognition. Fungal Genet Biol 2009; 46:632-41. [PMID: 19523529 DOI: 10.1016/j.fgb.2009.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Amylostereum areolatum is a filamentous fungus that grows through tip extension, branching and hyphal fusion. In the homokaryotic phase, the hyphae of different individuals are capable of fusing followed by heterokaryon formation, only if they have dissimilar allelic specificities at their mating-type (mat) loci. In turn, hyphal fusion between heterokaryons persists only when they share the same alleles at all of their heterokaryon incompatibility (het) loci. In this study we present the first genetic linkage map for A. areolatum, onto which the mat and het loci, as well as quantitative trait loci (QTLs) for mycelial growth rate are mapped. The recognition loci (mat-A and het-A) are positioned near QTLs associated with mycelial growth, suggesting that the genetic determinants influencing recognition and growth rate in A. areolatum are closely associated. This was confirmed when isolates associated with specific mat and het loci displayed significantly different mycelial growth rates. Although the link between growth and sexual recognition has previously been observed in other fungi, this is the first time that an association between growth and self-recognition has been shown.
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Affiliation(s)
- M A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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Ghazanfari T, Yaraee R, Farahnejad Z, Hakimzadeh H, Danialy F. In vitroeffect ofPleurotusfloridaon macrophage cell viability and nitric oxide production. FOOD AGR IMMUNOL 2009. [DOI: 10.1080/09540100902838198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Reproducible and controllable light induction of in vitro fruiting of the white-rot basidiomycete Pleurotus ostreatus. ACTA ACUST UNITED AC 2009; 113:552-8. [DOI: 10.1016/j.mycres.2008.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 11/27/2008] [Accepted: 12/16/2008] [Indexed: 11/22/2022]
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Pérez G, Pangilinan J, Pisabarro AG, Ramírez L. Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus. Appl Environ Microbiol 2009; 75:1427-36. [PMID: 19114509 PMCID: PMC2648151 DOI: 10.1128/aem.01889-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/21/2008] [Indexed: 01/19/2023] Open
Abstract
Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete Pleurotus ostreatus using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in P. ostreatus is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in Pleurotus contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi Neurospora crassa and Aspergillus terreus. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map.
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Affiliation(s)
- Gúmer Pérez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
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Pezzella C, Autore F, Giardina P, Piscitelli A, Sannia G, Faraco V. The Pleurotus ostreatus laccase multi-gene family: isolation and heterologous expression of new family members. Curr Genet 2008; 55:45-57. [DOI: 10.1007/s00294-008-0221-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/03/2008] [Accepted: 11/08/2008] [Indexed: 10/21/2022]
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46
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Labbé J, Zhang X, Yin T, Schmutz J, Grimwood J, Martin F, Tuskan GA, Le Tacon F. A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies. THE NEW PHYTOLOGIST 2008; 180:316-328. [PMID: 18783356 DOI: 10.1111/j.1469-8137.2008.02614.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A genetic linkage map for the ectomycorrhizal basidiomycete Laccaria bicolor was constructed from 45 sib-homokaryotic haploid mycelial lines derived from the parental S238N strain progeny. For map construction, 294 simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers were employed to identify and assay loci that segregated in backcross configuration. Using SNP, RAPD and SSR sequences, the L. bicolor whole-genome sequence (WGS) assemblies were aligned onto the linkage groups. A total of 37.36 Mbp of the assembled sequences was aligned to 13 linkage groups. Most mapped genetic markers used in alignment were colinear with the sequence assemblies, indicating that both the genetic map and sequence assemblies achieved high fidelity. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 13 linkage groups spanning 812 centiMorgans (cM) at an average distance of 2.76 cM between markers (range 1.9-17 cM). The WGS and the present linkage map represent an initial step towards the identification and cloning of quantitative trait loci associated with development and functioning of the ectomycorrhizal symbiosis.
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Affiliation(s)
- J Labbé
- UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - X Zhang
- Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA
- Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA
| | - T Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA
- Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA
| | - J Schmutz
- Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304, USA
| | - J Grimwood
- Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304, USA
| | - F Martin
- UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
| | - G A Tuskan
- Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6422, USA
- Joint Genome Institute, 2500 Mitchell St, Walnut Creek, CA 94250, USA
| | - F Le Tacon
- UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
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Quantitative linkage mapping of lignin-degrading enzymatic activities in Pleurotus ostreatus. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2007.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pisabarro AG, Perez G, Lavin JL, Ramirez L. Genetic networks for the functional study of genomes. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:249-63. [DOI: 10.1093/bfgp/eln026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Manzo-Sánchez G, Zapater MF, Luna-Martínez F, Conde-Ferráez L, Carlier J, James-Kay A, Simpson J. Construction of a genetic linkage map of the fungal pathogen of banana Mycosphaerella fijiensis, causal agent of black leaf streak disease. Curr Genet 2008; 53:299-311. [PMID: 18365202 DOI: 10.1007/s00294-008-0186-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 12/15/2022]
Abstract
A genetic linkage map of the fungal plant pathogen Mycosphaerella fijiensis, causal agent of black leaf streak disease of banana was developed. A cross between the isolates CIRAD86 (from Cameroon) and CIRAD139A (from Colombia) was analyzed using molecular markers and the MAT locus. The genetic linkage map consists of 298 AFLP and 16 SSR markers with 23 linkage groups, containing five or more markers, covering 1,879 cM. Markers are separated on average by around 5.9 cM. The MAT locus was shown to segregate in a 1:1 ratio but could not be successfully mapped. An estimate of the relation between physical size and genetic distance was approximately 39.0 kb/cM. The estimated total haploid genome size was calculated using the genetic mapping data at 4,298.2 cM. This is the first genetic linkage map reported for this important foliar pathogen of banana. The great utility of the map will be for anchoring contigs in the genome sequence, evolutionary studies in comparison with other fungi, to identify quantitative trait loci (QTLs) associated with aggressiveness or oxidative stress resistance and with the recently available genome sequence, for positional cloning.
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Affiliation(s)
- Gilberto Manzo-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130. Colonia Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
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50
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Chang SW, Jung G. The first linkage map of the plant-pathogenic basidiomyceteTyphula ishikariensis. Genome 2008; 51:128-36. [DOI: 10.1139/g07-097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Speckled snow mold, caused by the basidiomycete Typhula ishikariensis Imai, is one of the most prominent winter diseases on perennial grasses and cereal crops in the northern hemisphere. The first linkage map of T. ishikariensis was constructed using a population of 93 sibling monokaryons derived from a single dikaryotic hybrid isolate that was created by a hyphal fusion of two monokaryotic parental isolates. The parental isolates were produced from a pathogenic dikaryotic isolate collected from a golf course in Wisconsin. The two parents exhibit significant differences in the production of aerial mycelium and sclerotia, and in their aggressiveness on creeping bentgrass ( Agrostis stolonifera L.). A total of 251 loci were mapped, comprising 89 inter-simple sequence repeat (ISSR) and 160 random amplified polymorphic DNA (RAPD) markers along with 2 phenotype-based mating-type (MAT) loci. The MAT loci were mapped on linkage groups (LGs) 1 and 7. The markers were evenly distributed over 7 LGs, covering 436 cM with an average marker interval of 2.2 cM. Seven chromosomes were cytologically observed using germ tube bursting methods with acetocarmine staining. This reference linkage map of T. ishikariensis should provide a framework for the mapping of quantitatively controlled traits such as fungal growth, survival, and virulence/avirulence under low temperatures. The map should also be utilized for studying the genome organization of the cold-loving plant-pathogenic Typhula spp. and for comparative genome analysis among fungal taxa.
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Affiliation(s)
- S. W. Chang
- Department of Plant, Soil, and Insect Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - G. Jung
- Department of Plant, Soil, and Insect Sciences, University of Massachusetts, Amherst, MA 01003, USA
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