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Liu X, Li B, Cai J, Shi T, Yang Y, Feng Y, Huang G. Whole genome resequencing reveal patterns of genetic variation within Colletotrichum acutatum species complex from rubber trees in China. Fungal Genet Biol 2023; 167:103801. [PMID: 37196569 DOI: 10.1016/j.fgb.2023.103801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023]
Abstract
The Colletotrichum acutatum species complex possesses a diverse number of important traits, such as a wide host range and host preference, different modes of reproduction, and different strategies of host infection. Research using comparative genomics has attempted to find correlations between these traits. Here, we used multi-locus techniques and gene genealogical concordance analysis to investigate the phylogenetic relationships and taxonomic status of the Colletotrichum acutatum species complex using field isolates obtained from rubber trees. The results revealed that the dominant species was C. australisinense, followed by C. bannaense, while strain YNJH17109 was identified as C. laticiphilum. The taxonomic status of strains YNLC510 and YNLC511 was undetermined. Using whole-genome single nucleotide polymorphism data to analyze population structure, 18 strains of C. australisinense were subsequently divided into four populations, one of which was derived from an admixture of two populations. In addition, the strains LD1687, GD1628, and YNLC516, did not belong to any populations, and were considered to be admixtures of two or more populations. A split decomposition network analysis also provided evidence for genetic recombination within Colletotrichum acutatum species complex from rubber trees in China. Overall, a weak phylogeographic sub-structure was observed. Analysis also revealed significant differences in morphological characters and levels of virulence between populations.
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Affiliation(s)
- Xianbao Liu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Boxun Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Jimiao Cai
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Tao Shi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Yanli Feng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China
| | - Guixiu Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, Hainan 571101, PR China.
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Alkemade JA, Baroncelli R, Messmer MM, Hohmann P. Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose. MOLECULAR PLANT PATHOLOGY 2023; 24:616-627. [PMID: 37078402 DOI: 10.1111/mpp.13332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
- Centre for Studies on Bioinspired Agro-Enviromental Technology, Università di Napoli Federico II, Portici, 80055, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Bonaplanta, BioCrops Innovations SL, Manresa, Spain
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Cao X, Zhang Q, He Y, Che H, Lin Y, Luo D, West JS, Xu X. Genetic Analysis of Colletotrichum siamense Populations from Different Hosts and Counties in Hainan, China, Using Microsatellite Markers. PLANT DISEASE 2023; 107:60-66. [PMID: 35666218 DOI: 10.1094/pdis-03-22-0576-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Colletotrichum siamense was demonstrated as the dominant species among Colletotrichum spp. that infected rubber tree, areca palm, and coffee in Hainan, China. However, the extent of genetic differentiation within the species C. siamense in relation to geographical regions and host species is not known. In this study, 112 C. siamense isolates were genotyped with 12 microsatellite markers. In total, there were 99 multilocus genotypes. Results from permutational multivariate analysis of variance and analysis of molecular variance indicated that there was no significant genetic differentiation between fungal populations with respect to host, location (county), and year. Discriminant analysis of principal components and STRUCTURE analysis showed that C. siamense isolates grouped into three clusters; further analysis confirmed that there were significant (P < 0.001) genetic differences among the three clusters. However, each cluster had isolates from different hosts, counties, or years, supporting the lack of genetic differentiation with respect to host, county, and year. Statistical analyses of allelic associations indicated some evidence for recombination within the populations defined on the basis of host or county. The present findings provide insights into the genetic structure of C. siamense on the three perennial host species in Hainan and suggest that the disease on these three crops can be effectively considered as one disease and, hence, needs to be controlled simultaneously in mixed plantations.
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Affiliation(s)
- Xueren Cao
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Qun Zhang
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yongxiang He
- College of Plant Protection, Hainan University, Haikou 570228 China
| | - Haiyan Che
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yating Lin
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daquan Luo
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | | | - Xiangming Xu
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, U.K
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Colletotrichum species and complexes: geographic distribution, host range and conservation status. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00491-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Wilson AM, Lelwala RV, Taylor PWJ, Wingfield MJ, Wingfield BD. Unique patterns of mating pheromone presence and absence could result in the ambiguous sexual behaviors of Colletotrichum species. G3 (BETHESDA, MD.) 2021; 11:jkab187. [PMID: 34544120 PMCID: PMC8661429 DOI: 10.1093/g3journal/jkab187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/18/2021] [Indexed: 11/14/2022]
Abstract
Colletotrichum species are known to engage in unique sexual behaviors that differ significantly from the mating strategies of other filamentous ascomycete species. For example, most ascomycete fungi require the expression of both the MAT1-1-1 and MAT1-2-1 genes to induce sexual reproduction. In contrast, all isolates of Colletotrichum harbor only the MAT1-2-1 gene and yet, are capable of recognizing suitable mating partners and producing sexual progeny. The molecular mechanisms contributing to mating types and behaviors in Colletotrichum are, however, unknown. A comparative genomics approach analyzing 35 genomes, representing 31 Colletotrichum species and two Verticillium species, was used to elucidate a putative molecular mechanism underlying the unique sexual behaviors observed in Colletotrichum species. The existence of only the MAT1-2 idiomorph was confirmed across all species included in this study. Comparisons of the loci harboring the two mating pheromones and their cognate receptors revealed interesting patterns of gene presence and absence. The results showed that these genes have been lost multiple, independent times over the evolutionary history of this genus. These losses indicate that the pheromone pathway no longer plays an active role in mating type determination, suggesting an undiscovered mechanism by which mating partner recognition is controlled in these species. This further suggests that there has been a redirection of the underlying genetic mechanisms that regulate sexual development in Colletotrichum species. This research thus provides a foundation from which further interrogation of this topic can take place.
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Affiliation(s)
- Andi M Wilson
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0083, South Africa
| | - Ruvini V Lelwala
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul W J Taylor
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael J Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0083, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0083, South Africa
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