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S. Hirao A, Kumata A, Takagi T, Sasaki Y, Shigihara T, Kimura E, Kaneko S. Japanese “nameko” mushrooms (<i>Pholiota microspora</i>) produced via sawdust-based cultivation exhibit severe genetic bottleneck associated with a single founder. MYCOSCIENCE 2022; 63:79-87. [PMID: 37089630 PMCID: PMC10012341 DOI: 10.47371/mycosci.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/19/2022] [Accepted: 03/19/2022] [Indexed: 11/16/2022]
Abstract
Pholiota microspora ("nameko" in Japanese) is one of the most common edible mushrooms, especially in Japan, where sawdust-based cultivation is the most dominant method accounting for 99% of the production. The current strains for sawdust cultivation in Japan are considered to have been derived from a single wild strain collected from Fukushima, Japan, implying that commercial nameko mushrooms are derived from a severe genetic bottleneck. We tested this single founder hypothesis by developing 14 microsatellite markers for P. microspora to evaluate the genetic diversity of 50 cultivars and 73 wild strains isolated from across Japan. Microsatellite analysis demonstrated that sawdust-cultivated strains from Japan were significantly less genetically diverse than the wild strains, and the former displayed a significant bottleneck signature. Analyzing the genetic relationships among all genotypes also revealed that the sawdust-cultivated samples clustered into one monophyletic subgroup. Moreover, the sawdust-cultivated samples in Japan were more closely related than full-sibs. These results were consistent with the single founder hypothesis that suggests that all commercial nameko mushrooms produced in Japan are descendants of a single ancestor. Therefore, we conclude that cultivated P. microspora originated from a single domestication event that substantially reduced the diversity of commercial nameko mushrooms in Japan.
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Affiliation(s)
- Akira S. Hirao
- Faculty of Symbiotic Systems Science, Fukushima University
| | | | | | | | | | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University
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Merényi Z, Virágh M, Gluck-Thaler E, Slot JC, Kiss B, Varga T, Geösel A, Hegedüs B, Bálint B, Nagy LG. Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom forming fungi (Agaricomycetes). eLife 2022; 11:71348. [PMID: 35156613 PMCID: PMC8893723 DOI: 10.7554/elife.71348] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans, a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Emile Gluck-Thaler
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jason C Slot
- Department of Plant Pathology, Ohio State University, Columbus, United States
| | - Brigitta Kiss
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - András Geösel
- Department of Vegetable and Mushroom Growing, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
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Yin C, Fan X, Ma K, Chen Z, Shi D, Yao F, Gao H, Ma A. Identification and characterization of a novel light-induced promoter for recombinant protein production in Pleurotus ostreatus. J Microbiol 2019; 58:39-45. [PMID: 31686390 DOI: 10.1007/s12275-020-9230-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/26/2019] [Accepted: 09/29/2019] [Indexed: 11/30/2022]
Abstract
A lectin gene (plectin) with a high level of expression was previously identified by comparative transcriptome analysis of Pleurotus ostreatus. In this study, we cloned a 733-bp DNA fragment from the start codon of the plectin gene. Sequence analysis showed that the plectin promoter (Plp) region contained several eukaryotic transcription factor binding motifs, such as the TATA-box, four possible CAAT-box, light respon-siveness motifs and MeJA-responsiveness motifs. To deter-mine whether the Plp promoter was a light-regulated promoter, we constructed an expression vector with the fused egfp-hph fragment under the control of the Plp promoter and transformed P. ostreatus mycelia via Agrobacterium tunte-faciens. PCR and Southern blot analyses confirmed the Plp-egfp-hph fragment was integrated into the chromosomal DNA of transformants. qRT-PCR, egfp visualization, and intracellular egfp determination experiments showed the Plp promoter could be a light-induced promoter that may be suitable for P. ostreatus genetic engineering. This study lays the foundation for gene homologous expression in P. ostreatus.
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Affiliation(s)
- Chaomin Yin
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China. .,National Research and Development Center for Edible Fungi Processing (Wuhan), Wuhan, 430064, P. R. China.
| | - Xiuzhi Fan
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Kun Ma
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Zheya Chen
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Defang Shi
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Fen Yao
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China
| | - Hong Gao
- Institute of Agro-Products Processing and Nuclear-Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, P. R. China.,National Research and Development Center for Edible Fungi Processing (Wuhan), Wuhan, 430064, P. R. China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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What is cultivated oyster mushroom? Phylogenetic and physiological study of Pleurotus ostreatus and related taxa. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01515-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dai Y, Sun L, Yin X, Gao M, Zhao Y, Jia P, Yuan X, Fu Y, Li Y. Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment. Front Microbiol 2019; 10:2024. [PMID: 31551962 PMCID: PMC6734163 DOI: 10.3389/fmicb.2019.02024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Pleurotus eryngii (King Oyster) is one of the most highly prized edible mushrooms. Among the diverse varieties within P. eryngii, P. eryngii var. eryngii is the commonest one, with a worldwide distribution, while P. eryngii var. ferulae is only distributed in Europe and China, and is especially adapted to the Gobi Desert in Xinjiang Autonomous Region of China. However, little is known about the genome-wide pattern of evolution and adaptation to the divergent environments of P. eryngii. Here, we present the high-quality genome sequences of P. eryngii var. eryngii strain PEE81 originating from Europe and P. eryngii var. ferulae strain PEF12 originating from the Gobi Desert of China. The assembled genome sizes of PEE81 and PEF12 were 53.6 and 48.0 Mbp, respectively, which are larger than other reported genomes in the genus Pleurotus. We propose that the selective amplification of long terminal repeat (LTR) retrotransposons increases the genome size of the genus Pleurotus, and may play a key role in driving their rapid species diversification. Molecular clock analyses of five Pleurotus species, namely PEE81, PEF12, P. tuoliensis, P. ostreatus and P. cf. floridanus suggest that the divergence estimates of the genus Pleurotus over time scales ranged from ∼4 to ∼38 million years ago (Mya), and PEE81 and PEF12 diverged at ∼13 Mya. The whole genome resequencing of 33 geographically diverse strains of P. eryngii var. eryngii and var. ferulae was then performed and the genome variation among and within these two populations were investigated. Comparative analyses of these two populations detected several candidate genes related to stress responses and DNA repair that are putatively involved in adaptation to the Gobi Desert environment. These findings offer insights into genome evolution of the genus Pleurotus and provide valuable genomic resources for King Oyster mushroom breeding.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiaolei Yin
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Meng Gao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yitong Zhao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Peisong Jia
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Xinjiang, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
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Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers. Genes (Basel) 2019; 10:genes10040281. [PMID: 30959931 PMCID: PMC6523640 DOI: 10.3390/genes10040281] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.
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