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Li Z, Zhu Z, Qian K, Tang B, Han B, Zhong Z, Fu T, Zhou P, Stukenbrock EH, Martin FM, Yuan Z. Intraspecific diploidization of a halophyte root fungus drives heterosis. Nat Commun 2024; 15:5872. [PMID: 38997287 PMCID: PMC11245560 DOI: 10.1038/s41467-024-49468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/03/2024] [Indexed: 07/14/2024] Open
Abstract
How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.
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Affiliation(s)
- Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Zhiyong Zhu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
- Nanjing Forestry University, Nanjing, 100071, China
| | - Kun Qian
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng, 224002, China
| | - Baocai Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Zhenhui Zhong
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Tao Fu
- Shenzhen Zhuoyun Haizhi Medical Research Center Co., Ltd, Shenzhen, 518063, China
| | - Peng Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Francis M Martin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganisms, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
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Na Q, Zeng H, Hu Y, Ding H, Ke B, Zeng Z, Liu C, Cheng X, Ge Y. Morphological and phylogenetic analyses reveal five new species of Porotheleaceae (Agaricales, Basidiomycota) from China. MycoKeys 2024; 105:49-95. [PMID: 38708027 PMCID: PMC11066505 DOI: 10.3897/mycokeys.105.118826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The first occurrence of Marasmiellomycena and Pulverulina in the Chinese mycobiota are reported, M.tomentosa and P.flavoalba, two new species and M.albodescendens, a new combination, revealed by phylogenetic analyses and morphological study. These newly-recorded genera, Marasmiellomycena, which can be distinguished by their agaricoid basidiomata, dark-coloured stipe, sarcodimitic tramal structure, stipitipellis with yellow to yellowish-brown pigments and yellow-pigmented thick-walled caulocystidia and Pulverulina, which differs from other genera of Porotheleaceae by its pruinose stipe, decurrent lamellae, inamyloid basidiospores and absence of hymenial cystidia. We also formally describe three other new species of Porotheleaceae collected from Chinese temperate to subtropical zones of Fujian and Zhejiang Provinces: Clitocybulafuscostriata, Gerronemabrunneosquamulosum and Leucoinocybesubglobispora. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae, based on a multi-locus (ITS, nrLSU and rpb2) dataset. According to this analysis, Chrysomycena, Clitocybula, Delicatula, Hydropodia, Hydropus, Leucoinocybe, Marasmiellomycena, Megacollybia, Pulverulina, Trogia and Vizzinia are monophyletic. However, Gerronema is identified as polyphyletic and, additionally, Porotheleum does not form a monophyletic group either because Porotheleumparvulum and Porotheleumalbidum are "unassigned" in phylogenetic analysis. The results of our phylogenetic analyses, coupled with morphological observations, confirm recognition of these new taxa. Morphological descriptions, photographs, line drawings and comparisons with closely-related taxa are presented for the new species. A key to the 22 species belonging to nine genera of Porotheleaceae in China is also provided.
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Affiliation(s)
- Qin Na
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, ChinaNanjing Institute of Environmental SciencesNanjingChina
| | - Hui Ding
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing 210042, ChinaNanjing Institute of Environmental SciencesNanjingChina
| | - Binrong Ke
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Zhiheng Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
| | - Changjing Liu
- College of Criminal Science and Technology, Nanjing Police University, Nanjing 210042, ChinaNanjing Police UniversityNanjingChina
| | - Xianhao Cheng
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yupeng Ge
- Institute of Mycological Science and Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural SciencesFuzhouChina
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Li H, Xu J, Wang S, Wang P, Rao W, Hou B, Zhang Y. Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China. Genes (Basel) 2022; 13:genes13050854. [PMID: 35627240 PMCID: PMC9141859 DOI: 10.3390/genes13050854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.
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Affiliation(s)
- Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shaojuan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Pengfei Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
| | - Wanqin Rao
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Bin Hou
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Correspondence:
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Na Q, Hu Y, Zeng H, Song Z, Ding H, Cheng X, Ge Y. Updated taxonomy on Gerronema (Porotheleaceae, Agaricales) with three new taxa and one new record from China. MycoKeys 2022; 89:87-120. [PMID: 36760827 PMCID: PMC9849079 DOI: 10.3897/mycokeys.89.79864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/16/2022] [Indexed: 11/12/2022] Open
Abstract
Only three Gerronema (Porotheleaceae) species have been previously recorded in China. Here, we report collections of a fourth species in China: G.nemorale Har. Takah., which is widely distributed in Chinese temperate to subtropical zones. We also formally describe three new species, collected from Anhui, Fujian, and Zhejiang provinces: G.baishanzuense sp. nov., G.microcarpum sp. nov., and G.zhujian sp. nov. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae based on a multi-locus (ITS + nLSU) dataset. The results, which indicate that Gerronema is polyphyletic, support the taxonomic recognition of the three new species. Morphological descriptions, photographs, line drawings, and comparisons with closely related taxa are presented for the new and newly recorded species. A key to the seven species of Gerronema in China is also provided.
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Affiliation(s)
- Qin Na
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yaping Hu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, 8 Jiangwangmiao street, Nanjing 210042, ChinaNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Hui Zeng
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible Fungi, Fuzhou 350014, ChinaFujian Academy of Agricultural Sciences; National and Local Joint Engineering Research Center for Breeding & Cultivation of Features Edible FungiFuzhouChina
| | - Zhizhong Song
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Hui Ding
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, 8 Jiangwangmiao street, Nanjing 210042, ChinaNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Xianhao Cheng
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
| | - Yupeng Ge
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai 264025, ChinaLudong UniversityYantaiChina
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Taxonomic update of Clitocybula sensu lato with a new generic classification. Fungal Biol 2019; 123:431-447. [DOI: 10.1016/j.funbio.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/14/2019] [Accepted: 03/19/2019] [Indexed: 11/23/2022]
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Xu YC, Xie XX, Zhou ZY, Feng T, Liu JK. A new monoterpene from the poisonous mushroom Trogia venenata, which has caused Sudden Unexpected Death in Yunnan province, China. Nat Prod Res 2018; 32:2547-2552. [DOI: 10.1080/14786419.2018.1425851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ying-Chao Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Xia Xie
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Zhong-Yu Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Feng
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
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Ruibal MP, Triponez Y, Smith LM, Peakall R, Linde CC. Population structure of an orchid mycorrhizal fungus with genus-wide specificity. Sci Rep 2017; 7:5613. [PMID: 28717170 PMCID: PMC5514033 DOI: 10.1038/s41598-017-05855-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/02/2017] [Indexed: 12/02/2022] Open
Abstract
Fundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks). Another Tulasnella species (T. sphagneti) appears to be restricted to moist conditions of alpine sphagnum hammocks. The population genetic structure of the widespread species T. prima, was investigated at 10 simple sequence repeat (SSR) markers and at four cross-amplified SSR loci for T. sphagneti. For both taxa, no sharing of multilocus genotypes was found between sites, but clones were found within sites. Evidence for inbreeding within T. prima was found at 3 of 5 sites. Significant genetic differentiation was found within and between taxa. Significant local positive spatial genetic autocorrelation was detected among non-clonal isolates at the scale of two metres. Overall, the population genetic patterns indicated that in Tulasnella mating occurs by inbreeding and dispersal is typically restricted to short-distances.
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Affiliation(s)
- M P Ruibal
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Y Triponez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - L M Smith
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - R Peakall
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - C C Linde
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
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