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Liu S, Hou Y, Zheng K, Ma Q, Wen M, Shao S, Wu S. Exploring the diversity, bioactivity of endophytes, and metabolome in Synsepalum dulcificum. Front Microbiol 2024; 15:1258208. [PMID: 38476934 PMCID: PMC10929569 DOI: 10.3389/fmicb.2024.1258208] [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: 07/13/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Synsepalum dulcificum exhibits high edible and medicinal value; however, there have been no reports on the exploration of its endophyte resources. Here, we conducted analyses encompassing plant metabolomics, microbial diversity, and the biological activities of endophytic metabolites in S. dulcificum. High-throughput sequencing identified 4,913 endophytic fungal amplicon sequence variants (ASVs) and 1,703 endophytic bacterial ASVs from the roots, stems, leaves, flowers, and fruits of S. dulcificum. Fungi were classified into 5 phyla, 24 classes, 75 orders, 170 families, and 313 genera, while bacteria belonged to 21 phyla, 47 classes, 93 orders, 145 families, and 232 genera. Furthermore, there were significant differences in the composition and content of metabolites in different tissues of S. dulcificum. Spearman's correlation analysis of the differential metabolites and endophytes revealed that the community composition of the endophytes correlated with plant-rich metabolites. The internal transcribed spacer sequences of 105 isolates were determined, and phylogenetic analyses revealed that these fungi were distributed into three phyla (Ascomycota, Basidiomycota, and Mucoromycota) and 20 genera. Moreover, 16S rDNA sequencing of 46 bacteria revealed they were distributed in 16 genera in three phyla: Actinobacteria, Proteobacteria, and Firmicutes. The antimicrobial activities (filter paper method) and antioxidant activity (DPPH and ABTS assays) of crude extracts obtained from 68 fungal and 20 bacterial strains cultured in different media were evaluated. Additionally, the α-glucosidase inhibitory activity of the fungal extracts was examined. The results showed that 88.6% of the strains exhibited antimicrobial activity, 55.7% exhibited antioxidant activity, and 85% of the fungi exhibited α-glucosidase inhibitory activity. The research suggested that the endophytes of S. dulcificum are highly diverse and have the potential to produce bioactive metabolites, providing abundant species resources for developing antibiotics, antioxidants and hypoglycemic drugs.
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Affiliation(s)
- Sisi Liu
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Yage Hou
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Kaixuan Zheng
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Qian Ma
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Meng Wen
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Shicheng Shao
- Department of Gardening and Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, Yunnan, China
| | - Shaohua Wu
- Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
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Tchokponhoué DA, Achigan-Dako EG, Sognigbé N, Nyadanu D, Hale I, Odindo AO, Sibiya J. Genome-wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa. THE PLANT GENOME 2023; 16:e20299. [PMID: 36661287 DOI: 10.1002/tpg2.20299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack of understanding of its evolutionary history and current population structure. Here, we report for the first time the application of genome-wide single nucleotide polymorphism genotyping to a diverse panel of S. dulcificum accessions to depict the genetic diversity and population structure of the species in the Dahomey Gap (DG) and Upper Guinea (UG) regions to infer its evolutionary history. Our findings suggest low overall genetic diversity but strong population divergence within the species. Neighbor-joining analysis detected two genetic groups in the UG and DG regions, while STRUCTURE distinguished three genetic groups, corresponding to the UG, Western DG, and Central DG regions. Application of Monmonier's algorithm revealed the existence of a barrier disrupting connectivity between the UG and DG groups. The Western DG group consistently exhibited the highest levels of nucleotide and haplotype diversities, while that of the Central DG exhibited the lowest. Analyses of Tajima's D, Fu's Fs, and Achaz Y* statistics suggest that while both UG and Central DG groups likely experienced recent expansions, the Western DG group is at equilibrium. These findings suggest a geographical structuring of genetic variation which supports the conclusion of differential evolutionary histories among West African groups of S. dulcificum. These results provide foundational insights to guide informed breeding population development and design sustainable conservation strategies for this species.
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Affiliation(s)
- Dèdéou A Tchokponhoué
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - N'Danikou Sognigbé
- Laboratory of Genetics, Biotechnology and Seed Science (GBioS), School of Plant Sciences, University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
- Ecole d'Horticulture et d'Aménagement des Espaces Verts, Université Nationale d'Agriculture, Kétou, Republic of Benin
- World Vegetable Center, East and Southern Africa, Arusha, Tanzania
| | - Daniel Nyadanu
- Cocoa Research Institute of Ghana (CRIG), Akim Tafo, Ghana
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Alfred O Odindo
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Julia Sibiya
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Zhang W, Wang Z, Dan Z, Zhang L, Xu M, Yang G, Chai M, Li Z, Xie H, Cong L. Transcriptome Analysis of Fusarium Root-Rot-Resistant and -Susceptible Alfalfa (Medicago sativa L.) Plants during Plant–Pathogen Interactions. Genes (Basel) 2022; 13:genes13050788. [PMID: 35627172 PMCID: PMC9140628 DOI: 10.3390/genes13050788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/04/2022] Open
Abstract
Alfalfa (Medicago sativa L.) is a perennial leguminous forage cultivated globally. Fusarium spp.-induced root rot is a chronic and devastating disease affecting alfalfa that occurs in most production fields. Studying the disease resistance regulatory network and investigating the key genes involved in plant–pathogen resistance can provide vital information for breeding alfalfa that are resistant to Fusarium spp. In this study, a resistant and susceptible clonal line of alfalfa was inoculated with Fusarium proliferatum L1 and sampled at 24 h, 48 h, 72 h, and 7 d post-inoculation for RNA-seq analysis. Among the differentially expressed genes (DEGs) detected between the two clonal lines at the four time points after inoculation, approximately 81.8% were detected at 24 h and 7 d after inoculation. Many DEGs in the two inoculated clonal lines participated in PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) mechanisms. In addition, transcription factor families such as bHLH, SBP, AP2, WRKY, and MYB were detected in response to infection. These results are an important supplement to the few existing studies on the resistance regulatory network of alfalfa against Fusarium root rot and will help to understand the evolution of host–pathogen interactions.
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