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de Oliveira TC, Rodrigues PT, Early AM, Duarte AMRC, Buery JC, Bueno MG, Catão-Dias JL, Cerutti C, Rona LDP, Neafsey DE, Ferreira MU. Plasmodium simium: population genomics reveals the origin of a reverse zoonosis. J Infect Dis 2021; 224:1950-1961. [PMID: 33870436 DOI: 10.1093/infdis/jiab214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/14/2021] [Indexed: 11/12/2022] Open
Abstract
The population history of Plasmodium simium, which causes malaria in sylvatic Neotropical monkeys and humans along the Atlantic Coast of Brazil, remains disputed. Genetically diverse P. vivax populations from various sources, including the lineages that founded the species P. simium, are thought to have arrived in the Americas in separate migratory waves. However, here we find a minimal genome-level differentiation between P. simium and present-day New World P. vivax isolates, consistent with their common geographic origin and subsequent divergence on this continent. The meagre genetic diversity in P. simium samples from humans and monkeys implies a recent transfer from humans to non-human primates - a unique example of malaria as a reverse zoonosis of public health significance. Likely genomic signatures of P. simium adaptation to new hosts include the deletion of >40% of a key erythrocyte invasion ligand, PvRBP2a, which may have favored more efficient simian host cell infection.
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Affiliation(s)
- Thaís C de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ana Maria R C Duarte
- Laboratory of Biochemistry and Molecular Biology, Superintendency for the Control of Endemics (SUCEN), State Secretary of Health, São Paulo, Brazil.,Laboratory of Protozoology, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Julyana C Buery
- Department of Social Medicine, Center for Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Marina G Bueno
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.,Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - José L Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Crispim Cerutti
- Department of Social Medicine, Center for Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Luísa D P Rona
- Department of Cell Biology, Embryology, and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil.,National Council for Scientific and Technological Development, National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Chniba I, Boujemaa S, Mardassi BBA, Ben Abdelmoumen Mardassi B. Clonal dissemination of antibiotic resistance among Tunisian Mycoplasma gallisepticum isolates as revealed by gene-targeted sequencing analysis. Avian Dis 2020; 65:446278. [PMID: 33057595 DOI: 10.1637/aviandiseases-d-20-00080r1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 11/05/2022]
Abstract
SummaryTo date, very little is known about avian mycoplasma infections in Tunisia. Mycoplasma gallisepticum is one of the most economically significant pathogen for poultry in Tunisia and worldwide. Based on the paucity of data regarding the genetic profiles and antibacterial behavior of M. gallisepticum strains in Tunisia, the present study was conducted. Genetic typing and phylogenetic relationships of 40 M. gallisepticum strains (20 Tunisian isolates, 19 international strains collection, and S6 reference strain) were investigated by gene-targeted sequencing (GTS) using 4 loci ( pvpA , mgc2 , vlhA and the InterGenic Spacer Region (IGSR) between the 16S and the 23S rRNA genes). GTS reveals 12 STs that were found to spread over 2 clonal complexes (CC) and 5 singletons.Emergence of enrofloxacin and spiramycin resistance among M. gallisepticum local isolates have been revealed using the broth microdilution method. Causal mutations have been identified by sequencing the quinolone-resistance determining region (QRDR) and domain II and V of 23S rRNA as well as the rplD and rplV genes for enrofloxacine- and macrolide-resistant isolates, respectively. The emersion of antibiotic resistance to enrofloxacin and spiramycin has been identified as being related to a distinctive clonal complex formed by 4 different STs (ST2, ST3, ST4 and ST5) which would suggest that this phenotype was clonally disseminated.
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Affiliation(s)
- Imen Chniba
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Safa Boujemaa
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Institut Pasteur de Tunis Head of Mycoplasmas Unit Group of Mycoplasmas. Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development 13, Place Pasteur, B.P. 74.1002 Tunis, Belvédère TUNISIA Tunis 1002 00216 71844790
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Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme. Vet Microbiol 2019; 237:108422. [PMID: 31585641 DOI: 10.1016/j.vetmic.2019.108422] [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: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 11/22/2022]
Abstract
Mycoplasma flocculare is genetically closely related to M. hyopneumoniae, the etiologic agent of porcine enzootic pneumonia, and is frequently isolated with this second species. In this article, we report on the development of the first multilocus sequence typing (MLST) scheme for M. flocculare, based on three genes (adk, rpoB and tpiA). In total, 5022 bp of sequence were analyzed. MLST was used to characterize seven M. flocculare isolates and the reference strain. Eight distinct sequence types were defined, showing the great intraspecies variability of M. flocculare, and the high discriminatory power of the new typing method. The relative contribution of recombinations to the genomic evolution of M. flocculare was revealed by calculating the index of association (IA: 0.0185). This MLST scheme is now available for the acquisition of new knowledge on M. flocculare epidemiology via an online database comprising the DNA sequences of each allele, available at http://pubmlst.org/mflocculare/.
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Frézal L, Jacqua G, Neema C. Adaptation of a Fungal Pathogen to Host Quantitative Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:1554. [PMID: 30429860 PMCID: PMC6220312 DOI: 10.3389/fpls.2018.01554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/03/2018] [Indexed: 05/29/2023]
Abstract
Impact of host quantitative resistance on pathogen evolution is still poorly documented. In our study, we characterized the adaptation of the pathogenic fungus Colletotrichum gloeosporioides, to the quantitative resistance of its host, the water yam (Dioscorea alata). Genetic and pathogenic diversities of C. gloeosporioides populations were specified at the field scale. We used nuclear markers to describe fungal population structuring within and between six fields of three cultivars differently susceptible to the fungus. Strain aggressiveness was then quantified in the laboratory through cross-inoculation tests. The high level of genetic diversity and significant linkage disequilibrium revealed a significant influence of clonal reproduction in the C. gloeosporioides evolution. The recorded fungal migration between fields was weak (evidence for a dispersion mode via tubers rather than splashing dispersal), which provides the first molecular evidence for limited C. gloeosporioides migration via yam tuber exchanges. C. gloeosporioides's populations are adapted to their host resistance. The aggressiveness of the fungal clones seems to have evolved toward an accumulation of components specific to each host cultivar. Despite the remaining marks of adaptation to the former widely cultivated host, adaptation to current cultivars was clearly depicted.
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Affiliation(s)
- Lise Frézal
- INRA-URPV, Guadeloupe, France
- CNRS – ENS – INSERM, Institut de Biologie de l’Ecole Normale Supérieure, Paris, France
| | | | - Claire Neema
- UMR BGPI, Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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Phylogenetics of Mycoplasma hominis clinical strains associated with gynecological infections or infertility as disclosed by an expanded multilocus sequence typing scheme. Sci Rep 2018; 8:14854. [PMID: 30291332 PMCID: PMC6173709 DOI: 10.1038/s41598-018-33260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022] Open
Abstract
To our knowledge, the phylodistribution of M. hominis clinical strains associated with various pathological conditions of the urogenital tract has not been explored hitherto. Here we analyzed the genetic diversity and phylogenetic relationships among 59 M. hominis Tunisian clinical isolates, categorized as gynecological infections- or infertility-associated pathotypes. For this purpose, we developed an expanded multilocus sequence typing (eMLST) scheme, combining the previously reported multilocus sequence typing (MLST) loci (gyrB, tuf, ftsY, uvrA, gap) with a new selected set of putative virulence genes (p120’, vaa, lmp1, lmp3, p60), referred herein to as multi-virulence-locus sequence typing (MVLST) loci. In doing so, M. hominis population was segregated into two distinct genetic lineages, which were differentially associated with each pathotype. Such a clear dichotomy was supported by several phylogenetic and population genetic analysis tools. Recombination was found to take place, but not sufficient enough to break down the overall clonal population structure of M. hominis, most likely as a result of purifying selection, which accommodated the most fit clones. In sum, and owing to the eMLST scheme described herein, we provide insightful data on the phylogenetics of M. hominis, arguing for the existence of genetically differentiable urogenital pathotypes.
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Li W, Song Y, Zhong Z, Huang X, Wang C, Li C, Yang H, Liu H, Ren Z, Lan J, Wu K, Peng G. Population genetics of Enterocytozoon bieneusi in captive giant pandas of China. Parasit Vectors 2017; 10:499. [PMID: 29047380 PMCID: PMC5648467 DOI: 10.1186/s13071-017-2459-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/08/2017] [Indexed: 01/21/2023] Open
Abstract
Background Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. Results We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E. bieneusi population genetics. For multilocus genotype (MLG) analysis of E. bieneusi-positive isolates, the MS1, MS3, MS4, and MS7 microsatellite and minisatellite loci were amplified and sequenced in 48, 45, 50 and 47 specimens, respectively, generating ten, eight, nine and five types. We successfully amplified 36 specimens and sequenced all five loci, forming 24 MLGs. Multilocus sequence analysis revealed a strong and significant linkage disequilibrium (LD), indicating a clonal population. This result was further supported by measurements of pairwise intergenic LD and a standardized index of association (ISA) from allelic profile data. The analysis in STRUCTURE suggested three subpopulations in E. bieneusi, further confirmed using right’s fixation index (FST). Subpopulations 1 and 2 exhibited an epidemic structure, whereas subpopulation 3 had a clonal structure. Conclusions Our results describe E. bieneusi population genetics in giant pandas for the first time, improving the current understanding E. bieneusi epidemiology in the studied region. These data also benefit future studies exploring potential transmission risks from pandas to other animals, including humans.
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Affiliation(s)
- Wei Li
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Yuan Song
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Zhijun Zhong
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Xiangming Huang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | | | - Caiwu Li
- Wolong Giant Panda Base, Aba, Sichuan Province, China
| | - Haidi Yang
- Wolong Giant Panda Base, Aba, Sichuan Province, China
| | - Haifeng Liu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Zhihua Ren
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China
| | - Jingchao Lan
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | - Kongju Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, China
| | - Guangneng Peng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan Province, China.
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Fayette J, Raid R, Roberts PD, Jones JB, Pernezny K, Bull CT, Goss EM. Multilocus Sequence Typing of Strains of Bacterial Spot of Lettuce Collected in the United States. PHYTOPATHOLOGY 2016; 106:1262-1269. [PMID: 27359264 DOI: 10.1094/phyto-11-15-0302-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Studies on genetic diversity and recombination in bacterial pathogens are providing a better understanding of the mechanisms shaping bacterial diversity, which can affect disease control. Xanthomonas campestris pv. vitians, causal agent of bacterial leaf spot of lettuce, is a threat to the worldwide lettuce industry. We examined the genetic variation within a sample of 83 strains from California, Florida, and Ohio using multilocus sequence typing of six housekeeping genes, totaling 2.7 kb. Additionally, polymorphism in two virulence-related genes, hrpB2 and a putative glycosyl hydrolase, were examined. Based on housekeeping genes, we found three genetic groups of strains that were all able to induce the disease. These included strains collected from weeds and irrigation water that had haplotypes identical to strains from diseased lettuce. High linkage disequilibrium across the sequenced loci indicates that the pathogen is predominantly clonal but recombination has contributed to the observed sequence variation. Although there was significant genetic variation in X. campestris pv. vitians within and among sampled states, identical haplotypes were observed across all three states. This finding suggests that seedborne inoculum may contribute to the diversity of X. campestris pv. vitians in the United States. Knowledge of the genetic structure of the pathogen may be used for developing resistant lettuce varieties.
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Affiliation(s)
- Joubert Fayette
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Richard Raid
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Pamela D Roberts
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Jeffrey B Jones
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Ken Pernezny
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Carolee T Bull
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
| | - Erica M Goss
- First, second, and fifth authors: Everglades Research and Education Center, University of Florida Institute of Food and Agricultural Sciences (IFAS), Belle Glade; third author: Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee; first, second, third, fourth, fifth, and seventh authors: Department of Plant Pathology, University of Florida, Gainesville; sixth author: United States Department of Agriculture-Agricultural Research Service, Pacific West Area, 1636 E. Alisal St., Salinas, CA; and seventh author: Emerging Pathogens Institute, University of Florida, Gainesville
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Genetically Determined Response to Artemisinin Treatment in Western Kenyan Plasmodium falciparum Parasites. PLoS One 2016; 11:e0162524. [PMID: 27611315 PMCID: PMC5017781 DOI: 10.1371/journal.pone.0162524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/24/2016] [Indexed: 12/16/2022] Open
Abstract
Genetically determined artemisinin resistance in Plasmodium falciparum has been described in Southeast Asia. The relevance of recently described Kelch 13-propeller mutations for artemisinin resistance in Sub-Saharan Africa parasites is still unknown. Southeast Asia parasites have low genetic diversity compared to Sub-Saharan Africa, where parasites are highly genetically diverse. This study attempted to elucidate whether genetics provides a basis for discovering molecular markers in response to artemisinin drug treatment in P. falciparum in Kenya. The genetic diversity of parasites collected pre- and post- introduction of artemisinin combination therapy (ACT) in western Kenya was determined. A panel of 12 microsatellites and 91 single nucleotide polymorphisms (SNPs) distributed across the P. falciparum genome were genotyped. Parasite clearance rates were obtained for the post-ACT parasites. The 12 microsatellites were highly polymorphic with post-ACT parasites being significantly more diverse compared to pre-ACT (p < 0.0001). The median clearance half-life was 2.55 hours for the post-ACT parasites. Based on SNP analysis, 15 of 90 post-ACT parasites were single-clone infections. Analysis revealed 3 SNPs that might have some causal association with parasite clearance rates. Further, genetic analysis using Bayesian tree revealed parasites with similar clearance phenotypes were more closely genetically related. With further studies, SNPs described here and genetically determined response to artemisinin treatment might be useful in tracking artemisinin resistance in Kenya.
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Mohd Abd Razak MR, Sastu UR, Norahmad NA, Abdul-Karim A, Muhammad A, Muniandy PK, Jelip J, Rundi C, Imwong M, Mudin RN, Abdullah NR. Genetic Diversity of Plasmodium falciparum Populations in Malaria Declining Areas of Sabah, East Malaysia. PLoS One 2016; 11:e0152415. [PMID: 27023787 PMCID: PMC4811561 DOI: 10.1371/journal.pone.0152415] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
Malaysia has a national goal to eliminate malaria by 2020. Understanding the genetic diversity of malaria parasites in residual transmission foci can provide invaluable information which may inform the intervention strategies used to reach elimination targets. This study was conducted to determine the genetic diversity level of P. falciparum isolates in malaria residual foci areas of Sabah. Malaria active case detection was conducted in Kalabakan and Kota Marudu. All individuals in the study sites were screened for malaria infection by rapid diagnostic test. Blood from P. falciparum-infected individuals were collected on filter paper prior to DNA extraction. Genotyping was performed using merozoite surface protein-1 (MSP-1), merozoite surface protein-2 (MSP-2), glutamate rich protein (GLURP) and 10 neutral microsatellite loci markers. The size of alleles, multiplicity of infection (MOI), mean number of alleles (Na), expected heterozygosity (He), linkage disequilibrium (LD) and genetic differentiation (FST) were determined. In Kalabakan, the MSP-1 and MSP-2 alleles were predominantly K1 and FC27 family types, respectively. The GLURP genotype VI (751-800 bp) was predominant. The MOI for MSP-1 and MSP-2 were 1.65 and 1.20, respectively. The Na per microsatellite locus was 1.70. The He values for MSP-1, MSP-2, GLURP and neutral microsatellites were 0.17, 0.37, 0.70 and 0.33, respectively. In Kota Marudu, the MSP-1 and MSP-2 alleles were predominantly MAD20 and 3D7 family types, respectively. The GLURP genotype IV (651-700 bp) was predominant. The MOI for both MSP-1 and MSP-2 was 1.05. The Na per microsatellite locus was 3.60. The He values for MSP-1, MSP-2, GLURP and neutral microsatellites were 0.24, 0.25, 0.69 and 0.30, respectively. A significant LD was observed in Kalabakan (0.495, p<0.01) and Kota Marudu P. falciparum populations (0.601, p<0.01). High genetic differentiation between Kalabakan and Kota Marudu P. falciparum populations was observed (FST = 0.532). The genetic data from the present study highlighted the limited diversity and contrasting genetic pattern of P. falciparum populations in the malaria declining areas of Sabah.
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Affiliation(s)
| | - Umi Rubiah Sastu
- Herbal Medicine Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Nor Azrina Norahmad
- Herbal Medicine Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Abass Abdul-Karim
- Zonal Public Health Laboratory, Tamale Teaching Hospital, Tamale, Northern Region, Ghana, West Africa
| | - Amirrudin Muhammad
- Herbal Medicine Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Prem Kumar Muniandy
- Herbal Medicine Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Jenarun Jelip
- Sabah State Health Department, Rumah Persekutuan, Kota Kinabalu, Sabah, Malaysia
| | - Christina Rundi
- Sabah State Health Department, Rumah Persekutuan, Kota Kinabalu, Sabah, Malaysia
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rose Nani Mudin
- Vector Borne Disease Sector, Disease Control Division, Ministry of Health, Federal Government Administrative Centre, Putrajaya, Malaysia
| | - Noor Rain Abdullah
- Herbal Medicine Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia
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Ingasia LA, Cheruiyot J, Okoth SA, Andagalu B, Kamau E. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya. INFECTION GENETICS AND EVOLUTION 2015; 39:372-380. [PMID: 26472129 DOI: 10.1016/j.meegid.2015.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
Abstract
Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p<0.0001) whereas Kisii had the least significant index of association values (0.03; p<0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.
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Affiliation(s)
- Luicer A Ingasia
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Jelagat Cheruiyot
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Sheila Akinyi Okoth
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States; Atlanta Research and Education Foundation/VA Medical Center, Decatur, GA, United States
| | - Ben Andagalu
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya
| | - Edwin Kamau
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya.
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Kuzmanović N, Biondi E, Bertaccini A, Obradović A. Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe. J Appl Microbiol 2015; 119:786-96. [PMID: 26032990 DOI: 10.1111/jam.12858] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/21/2015] [Accepted: 05/21/2015] [Indexed: 11/27/2022]
Abstract
AIMS To analyse genetic diversity and epidemiological relationships among 54 strains of Allorhizobium vitis isolated in Europe during an 8-year period and to assess the relative contribution of mutation and recombination in shaping their diversity. METHODS AND RESULTS By using random amplified polymorphic DNA (RAPD) PCR, strains studied were distributed into 12 genetic groups. Sequence analysis of dnaK, gyrB and recA housekeeping genes was employed to characterize a representative subcollection of 28 strains. A total of 15 different haplotypes were found. Nucleotide sequence analysis suggested the presence of recombination events in A. vitis, particularly affecting dnaK locus. Although prevalence of mutation over recombination was found, impact of recombination was about two times greater than mutation in the evolution of the housekeeping genes analysed. CONCLUSIONS The RAPD analysis indicated high degree of genetic diversity among the strains. However, the most abundant RAPD group was composed of 35 strains, which could lead to the conclusion that they share a common origin and were distributed by the movement of infected grapevine planting material as a most common way of crossing long distances. Furthermore, it seems that recombination is acting as an important driving force in the evolution of A. vitis. As no substantial evidence of recombination was detected within recA gene fragment, this phylogenetic marker could be reliable to characterize phylogenetic relationships among A. vitis strains. SIGNIFICANCE AND IMPACT OF THE STUDY We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis.
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Affiliation(s)
- N Kuzmanović
- University of Belgrade-Faculty of Agriculture, Belgrade, Serbia
| | - E Biondi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - A Bertaccini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - A Obradović
- University of Belgrade-Faculty of Agriculture, Belgrade, Serbia
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Oyebola MK, Idowu ET, Nyang H, Olukosi YA, Otubanjo OA, Nwakanma DC, Awolola ST, Amambua-Ngwa A. Microsatellite markers reveal low levels of population sub-structuring of Plasmodium falciparum in southwestern Nigeria. Malar J 2014; 13:493. [PMID: 25496185 PMCID: PMC4300683 DOI: 10.1186/1475-2875-13-493] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic diversity studies provide evidence of Plasmodium falciparum differentiation that could affect fitness and adaptation to drugs and target antigens for vaccine development. This study describes the genetic structure of P. falciparum populations in urban and rural sites from southwestern Nigeria. METHODOLOGY Ten neutral microsatellite loci were genotyped in 196 P. falciparum infections from three localities: Aramoko-Ekiti, a rural community; Lekki, an urban location and Badagry, a peri-urban border settlement. Analysis was performed on the genetic diversity, linkage disequilibrium, population structure and inter-population differentiation. RESULTS Allelic diversity values were similar across all populations, with mean expected heterozygosity (HE) values between 0.65 and 0.79. No matching multilocus haplotypes were found and analysis of multilocus LD showed no significant index of association. Genetic differentiation between populations was low (ΦPT = 0.017). CONCLUSION The absence of detectable population structure of P. falciparum in southwestern Nigeria is evident in the lack of significant differentiation between populations separated by about 200 km. This implies that a fairly uniform malaria control strategy may be effective over a wide geographic range in this highly endemic region. However, more wide-scale survey across the country will be required to inform malaria control in this large and densely populated endemic region.
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Dixit J, Arunyawat U, Huong NT, Das A. Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus. Mol Ecol 2014; 23:5599-618. [PMID: 25266341 DOI: 10.1111/mec.12943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 01/11/2023]
Abstract
Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.
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Affiliation(s)
- Jyotsana Dixit
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
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Abstract
Neisseria gonorrhoeae and Neisseria meningitidis are closely related organisms that cause the sexually transmitted infection gonorrhea and serious bacterial meningitis and septicemia, respectively. Both species possess multiple mechanisms to alter the expression of surface-exposed proteins through the processes of phase and antigenic variation. This potential for wide variability in surface-exposed structures allows the organisms to always have subpopulations of divergent antigenic types to avoid immune surveillance and to contribute to functional variation. Additionally, the Neisseria are naturally competent for DNA transformation, which is their main means of genetic exchange. Although bacteriophages and plasmids are present in this genus, they are not as effective as DNA transformation for horizontal genetic exchange. There are barriers to genetic transfer, such as restriction-modification systems and CRISPR loci, that limit particular types of exchange. These host-restricted pathogens illustrate the rich complexity of genetics that can help define the similarities and differences of closely related organisms.
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Affiliation(s)
- Ella Rotman
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611; ,
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Benavides JA, Cross PC, Luikart G, Creel S. Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling. Evol Appl 2014; 7:774-87. [PMID: 25469159 PMCID: PMC4227858 DOI: 10.1111/eva.12173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 04/30/2014] [Indexed: 12/12/2022] Open
Abstract
Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced.
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Affiliation(s)
| | - Paul C Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center Bozeman, MT, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana Polson, MT, USA
| | - Scott Creel
- Department of Ecology, Montana State University Bozeman, MT, USA
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Multilocus sequence typing of Mycoplasma hyorhinis strains identified by a real-time TaqMan PCR assay. J Clin Microbiol 2014; 52:1664-71. [PMID: 24622092 DOI: 10.1128/jcm.03437-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A real-time TaqMan PCR assay based on the gene encoding the protein p37 was developed to detect Mycoplasma hyorhinis. Its specificity was validated with 29 epidemiologically unrelated M. hyorhinis strains (28 field strains and one reference strain) and other mycoplasma species or with other microorganisms commonly found in pigs. The estimated detection limit of this qPCR assay was 125 microorganism equivalents/μl. The same 29 epidemiologically unrelated M. hyorhinis strains and four previously fully sequenced strains were typed by two portable typing methods, the sequencing of the p37 gene and a multilocus sequence typing (MLST) scheme. The first method revealed 18 distinct nucleotide sequences and insufficient discriminatory power (0.934). The MLST scheme was developed with the sequenced genomes of the M. hyorhinis strains HUB-1, GDL-1, MCLD, and SK76 and based on the genes dnaA, rpoB, gyrB, gltX, adk, and gmk. In total, 2,304 bp of sequence was analyzed for each strain. MLST was capable of subdividing the 33 strains into 29 distinct sequence types. The discriminatory power of the method was >0.95, which is the threshold value for interpreting typing results with confidence (D=0.989). Population analysis showed that recombination in M. hyorhinis occurs and that strains are diverse but with a certain clonality (one unique clonal complex was identified). The new qPCR assay and the robust MLST scheme are available for the acquisition of new knowledge on M. hyorhinis epidemiology. A web-accessible database has been set up for the M. hyorhinis MLST scheme at http://pubmlst.org/mhyorhinis/.
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Karim MR, Wang R, He X, Zhang L, Li J, Rume FI, Dong H, Qi M, Jian F, Zhang S, Sun M, Yang G, Zou F, Ning C, Xiao L. Multilocus sequence typing of Enterocytozoon bieneusi in nonhuman primates in China. Vet Parasitol 2013; 200:13-23. [PMID: 24388499 DOI: 10.1016/j.vetpar.2013.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/29/2013] [Accepted: 12/06/2013] [Indexed: 10/25/2022]
Abstract
To infer population genetics of Enterocytozoon bieneusi in nonhuman primates (NHPs), 126 positive specimens in 839 fecal specimens from 23 NHP species in China based on ITS locus were used, belonging to genotypes Type IV, D, Peru8, Henan V, Peru11, PigEBITS7 and 3 novel ones (CM1, CM2 and CM3). Multilocus sequence typing employing four micro and minisatellites (MS1, MS3, MS4 and MS7) and ITS were used to analyze population structure of 85 isolates successfully amplified at all five loci, which yielded 59 multilocus genotypes. Linkage disequilibrium (LD) was measured using both multilocus sequences and allelic profile data. The observation of strong and significant LD with limited recombination in multilocus sequence analysis indicated the presence of overall clonal population structure of E. bieneusi, which was supported by allelic profile data analysis. Fu's selective neutrality test demonstrated the absence of neutral mutations and molecular selection. The population structure of common ITS genotypes (CM1, Type IV and D) was compared. Strong LD in multilocus sequence analysis versus insignificant LD and/or LE in allelic profile data analysis implied epidemic population in common ITS genotypes. No significant genetic isolation was evidenced by either phylogenetic or substructural analyses. The population genetics was also compared among the sub-population 1 (contained mainly genotype Type IV), sub-population 2 (contained mainly genotypes CM1 and D), sub-population 3 (contained mixed genotypes) and sub-population 4 (contained genotype Henan V). The presence of strong LD in multilocus data analysis with insignificant LD and/or LE in allele profile data analysis suggested the epidemic population in sub-populations.
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Affiliation(s)
- Md Robiul Karim
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoyi He
- Xiangya School of Medicine, Central South University, 410013, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Jian Li
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Farzana Islam Rume
- Department of Microbiology, Patuakhali Science and Technology University, Patuakhali 8602, Bangladesh
| | - Haiju Dong
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Meng Qi
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Fuchun Jian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Sumei Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingfei Sun
- Institute of Veterinary Medicine, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guangyou Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Yaan 625014, China
| | - Fengcai Zou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changshen Ning
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Lihua Xiao
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Kuhls K, Cupolillo E, Silva SO, Schweynoch C, Côrtes Boité M, Mello MN, Mauricio I, Miles M, Wirth T, Schönian G. Population structure and evidence for both clonality and recombination among Brazilian strains of the subgenus Leishmania (Viannia). PLoS Negl Trop Dis 2013; 7:e2490. [PMID: 24205418 PMCID: PMC3814519 DOI: 10.1371/journal.pntd.0002490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 09/08/2013] [Indexed: 12/03/2022] Open
Abstract
Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symptoms ranging from cutaneous leishmaniases (CL) with single or few lesions, disseminated CL (DL) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis (MCL). In this population genetics study, 37 strains of L. (V.) guyanensis, 63 of L. (V.) braziliensis, four of L. (V.) shawi, six of L. (V.) lainsoni, seven of L. (V.) naiffi, one each of L. (V.) utingensis and L. (V.) lindenbergi, and one L. (V.) lainsoni/L. naiffi hybrid from different endemic foci in Brazil were examined for variation at 15 hyper-variable microsatellite markers. Methodology/Principal findings: The multilocus microsatellite profiles obtained for the 120 strains were analysed using both model- and distance-based methods. Significant genetic diversity was observed for all L. (Viannia) strains studied. The two cluster analysis approaches identified two principal genetic groups or populations, one consisting of strains of L. (V.) guyanensis from the Amazon region and the other of strains of L. (V.) braziliensis isolated along the Atlantic coast of Brazil. A third group comprised a heterogeneous assembly of species, including other strains of L. braziliensis isolated from the north of Brazil, which were extremely polymorphic. The latter strains seemed to be more closely related to those of L. (V.) shawi, L. (V.) naiffi, and L. (V.) lainsoni, also isolated in northern Brazilian foci. The MLMT approach identified an epidemic clone consisting of 13 strains of L. braziliensis from Minas Gerais, but evidence for recombination was obtained for the populations of L. (V.) braziliensis from the Atlantic coast and for L. (V.) guyanensis. Conclusions/Significance: Different levels of recombination versus clonality seem to occur within the subgenus L. (Viannia). Though clearly departing from panmixia, sporadic, but long-term sustained recombination might explain the tremendous genetic diversity and limited population structure found for such L. (Viannia) strains. Cutaneous leishmaniasis (CL) constitutes a significant public health problem in all federal states of Brazil. Most cases are caused by parasites of the subgenus Leishmania (Viannia) which can cause a variety of clinical symptoms ranging from single or few lesions, disseminated CL with multiple lesions, to disfiguring forms of mucocutaneous leishmaniasis. This study has used a multilocus microsatellite typing approach for exploring the genetic diversity and population structure among 120 strains representing different subgenus L. (Viannia) species and different Brazilian CL foci. Genetic diversity within the subgenus was much higher than expected, especially within L. (V.) braziliensis, L. (V.) shawi, L. (V.) naiffi, and L. (V.) lainsoni which were all from the north of Brazil. These strains could not be assigned to well-defined populations, but presented a rather loosely associated group. Strains of L. (V.) braziliensis isolated along the Atlantic coast of Brazil and strains of L. (V.) guyanensis formed, however, two clearly separated populations exhibiting remarkable levels of sexual exchange. The latter finding is in contrast to previous studies suggesting clonal modes of propagation or inbreeding for natural populations of Leishmania parasites and might explain the genetic heterogeneity and limited population structure for Brazilian strains of subgenus L. (Viannia) observed in this study.
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Affiliation(s)
- Katrin Kuhls
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Soraia O. Silva
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carola Schweynoch
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mariana Côrtes Boité
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Maria N. Mello
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabel Mauricio
- Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael Miles
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Thierry Wirth
- Ecole Pratique des Hautes Etudes, Muséum National d'Histoire Naturelle, Département de Systématique et Évolution, UMR-CNRS 7205, Paris, France
| | - Gabriele Schönian
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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Larrañaga N, Mejía RE, Hormaza JI, Montoya A, Soto A, Fontecha GA. Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border. Malar J 2013; 12:354. [PMID: 24093629 PMCID: PMC3851272 DOI: 10.1186/1475-2875-12-354] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/02/2013] [Indexed: 01/01/2023] Open
Abstract
Background The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Methods Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. Results There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (He) results were similarly low for both populations. A moderate differentiation was revealed by the FST index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America.
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Affiliation(s)
- Nerea Larrañaga
- Instituto de Investigacion en Microbiologia, Escuela de Microbiologia, UNAH, Tegucigalpa, Honduras.
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Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae). PLoS One 2013; 8:e70162. [PMID: 23894608 PMCID: PMC3718774 DOI: 10.1371/journal.pone.0070162] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022] Open
Abstract
The present study investigated the genetic diversity, population structure, FST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.
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McEwen JR, Vamosi JC, Rogers SM. Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae). PLoS One 2013; 8:e68889. [PMID: 23874801 PMCID: PMC3715535 DOI: 10.1371/journal.pone.0068889] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 06/02/2013] [Indexed: 11/18/2022] Open
Abstract
Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.
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Affiliation(s)
- Jamie R McEwen
- University of British Columbia, Department of Botany, Vancouver, BC, Canada.
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Fournier E, Gladieux P, Giraud T. The 'Dr Jekyll and Mr Hyde fungus': noble rot versus gray mold symptoms of Botrytis cinerea on grapes. Evol Appl 2013; 6:960-9. [PMID: 24062804 PMCID: PMC3779096 DOI: 10.1111/eva.12079] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 04/08/2013] [Indexed: 11/29/2022] Open
Abstract
Many cryptic species have recently been discovered in fungi, especially in fungal plant pathogens. Cryptic fungal species co-occurring in sympatry may occupy slightly different ecological niches, for example infecting the same crop plant but specialized on different organs or having different phenologies. Identifying cryptic species in fungal pathogens of crops and determining their ecological specialization are therefore crucial for disease management. Here, we addressed this question in the ascomycete Botrytis cinerea, the agent of gray mold on a wide range of plants. On grape, B. cinerea causes severe damage but is also responsible for noble rot used for processing sweet wines. We used microsatellite genotyping and clustering methods to elucidate whether isolates sampled on gray mold versus noble rot symptoms in three French regions belong to genetically differentiated populations. The inferred population structure matched geography rather than the type of symptom. Noble rot symptoms therefore do not seem to be caused by a specific B. cinerea population but instead seem to depend essentially on microclimatic conditions, which has applied consequences for the production of sweet wines.
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Affiliation(s)
- Elisabeth Fournier
- Biologie et Génétique des Interactions Plante-Parasite, INRA-CIRAD-SupAgro Montpellier Cedex 5, France
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Li W, Cama V, Akinbo FO, Ganguly S, Kiulia NM, Zhang X, Xiao L. Multilocus sequence typing of Enterocytozoon bieneusi: Lack of geographic segregation and existence of genetically isolated sub-populations. INFECTION GENETICS AND EVOLUTION 2013; 14:111-9. [DOI: 10.1016/j.meegid.2012.11.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/16/2012] [Accepted: 11/27/2012] [Indexed: 11/29/2022]
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Tahvanainen P, Alpermann TJ, Figueroa RI, John U, Hakanen P, Nagai S, Blomster J, Kremp A. Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga. PLoS One 2012; 7:e53602. [PMID: 23300940 PMCID: PMC3534129 DOI: 10.1371/journal.pone.0053602] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/30/2012] [Indexed: 11/18/2022] Open
Abstract
This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F(ST)) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.
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Affiliation(s)
- Pia Tahvanainen
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland.
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Guglielmo F, Michelotti S, Nicolotti G, Gonthier P. Population structure analysis provides insights into the infection biology and invasion strategies of Kretzschmaria deusta in trees. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2012.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang T, Chen G, Zan Q, Wang C, Su YJ. AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha. PLoS One 2012; 7:e41310. [PMID: 22829939 PMCID: PMC3400595 DOI: 10.1371/journal.pone.0041310] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.
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Affiliation(s)
- Ting Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Guopei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qijie Zan
- Shenzhen Wildlife Rescue and Rehabilitation Center, Shenzhen, China
| | - Chunbo Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-juan Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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Khan N, Chittoria A, Pande V, Jaiswal YK, Das A. Development of multilocus putatively neutral DNA markers in the X-chromosome for population genetic studies in humans. Ann Hum Biol 2012; 39:281-9. [PMID: 22656191 DOI: 10.3109/03014460.2012.689326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND It has now been well documented that the type (coding, non-coding) and location (nuclear, mitochondrial etc.) of genetic markers heavily influence evolutionary inferences; realistic assumptions can be drawn if multiple putatively neutral DNA fragments spread across the genome are used. AIM To infer human population history, Single Nucleotide Polymorphisms (SNPs), located in the non-coding regions of different genes in the X-chromosome have been developed as 'putatively neutral markers'. SUBJECTS AND METHODS A population sample consisting of 16 male individuals from the western part of India was utilized for sequencing eight DNA fragments located in introns of three genes (Duchenne muscular dystrophy, Factor IX and Pyruvate dehydrogenase E1 sub-unit) on the human X-chromosome. PCR amplification and DNA sequencing confirmed the polymorphic status of all the fragments. RESULTS Twenty nine SNPs were found to be segregating in the Western Indian population samples. Using these SNPs the nucleotide diversity and demographic parameters of the Western Indian population were estimated. Several tests of neutrality ascertained that all eight fragments evolve putatively neutrally. Further, linkage disequilibrium analyses confirmed this fact. CONCLUSION All eight DNA fragments seem to bear the characteristics to be considered as 'putatively neutral genetic markers' and thus, could be utilized for inference of human population and demographic histories.
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Affiliation(s)
- Naazneen Khan
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi - 110077, India
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Wicker E, Lefeuvre P, de Cambiaire JC, Lemaire C, Poussier S, Prior P. Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA. THE ISME JOURNAL 2012; 6:961-74. [PMID: 22094345 PMCID: PMC3329105 DOI: 10.1038/ismej.2011.160] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 01/14/2023]
Abstract
We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during R. solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral phylotype, phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination and evidences of long-distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether R. solanacearum lineages will eventually evolve in distinct species remains an open question. The intensification of cropping and increase of geographical dispersion may favour situations of phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool.
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Affiliation(s)
- Emmanuel Wicker
- CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France.
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Multilocus sequence typing scheme for the characterization of 936-like phages infecting Lactococcus lactis. Appl Environ Microbiol 2012; 78:4646-53. [PMID: 22522686 DOI: 10.1128/aem.00931-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis phage infections are costly for the dairy industry because they can slow down the fermentation process and adversely impact product safety and quality. Although many strategies have been developed to better control phage populations, new virulent phages continue to emerge. Thus, it is beneficial to develop an efficient method for the routine identification of new phages within a dairy plant to rapidly adapt antiphage tactics. Here, we present a multilocus sequence typing (MLST) scheme for the characterization of the 936-like phages, the most prevalent phage group infecting L. lactis strains worldwide. The proposed MLST system targets the internal portion of five highly conserved genomic sequences belonging to the packaging, morphogenesis, and lysis modules. Our MLST scheme was used to analyze 100 phages with different restriction fragment length polymorphism (RFLP) patterns isolated from 11 different countries between 1971 and 2010. PCR products were obtained for all the phages analyzed, and sequence analysis highlighted the high discriminatory power of the MLST system, detecting 93 different sequence types. A conserved locus within the lys gene (coding for endolysin) was the most discriminative, with 65 distinct alleles. The locus within the mcp gene (major capsid protein) was the most conserved (54 distinct alleles). Phylogenetic analyses of the concatenated sequences exhibited a strong concordance of the clusters with the phage host range, indicating the clonal evolution of these phages. A public database has been set up for the proposed MLST system, and it can be accessed at http://pubmlst.org/bacteriophages/.
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Li W, Cama V, Feng Y, Gilman RH, Bern C, Zhang X, Xiao L. Population genetic analysis of Enterocytozoon bieneusi in humans. Int J Parasitol 2012; 42:287-93. [PMID: 22534008 DOI: 10.1016/j.ijpara.2012.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/26/2012] [Accepted: 01/29/2012] [Indexed: 10/28/2022]
Abstract
Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi.
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Affiliation(s)
- Wei Li
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Wang T, Chen G, Zan Q, Wang C, Su YJ. AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha. PLoS One 2012. [PMID: 22829939 DOI: 10.1371/journal.pone.0041310e41310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.
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Affiliation(s)
- Ting Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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McInnes LM, Dargantes AP, Ryan UM, Reid SA. Microsatellite typing and population structuring of Trypanosoma evansi in Mindanao, Philippines. Vet Parasitol 2011; 187:129-39. [PMID: 22230026 DOI: 10.1016/j.vetpar.2011.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 12/03/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
Abstract
Trypanosoma evansi, a blood-borne protozoan parasite with an extensive geographical range is the causative agent of the livestock disease known as surra. A total of 140 out of 179 T. evansi isolates collected between 2006 and 2007 from 44 villages (comprising of 16 reported surra outbreaks) in 3 provinces (Agusan del Sur (ADS), Surigao del Sur (SDS) and Agusan del Norte (ADN)) in Mindanao, Philippines were each successfully genotyped using a suite of 7 polymorphic microsatellites. The study identified 16 multi locus genotypes (MLG) within the T. evansi isolates and evidence of the spread of surra outbreaks from one village to another, most likely due to the movement of infected animals. Genotyping provided evidence of population sub-structuring with 3 populations (I, II and III (only 1 isolate)) identified. The most abundant population was II, which was the predominant population in ADS and SDS (p=0.022). In addition, buffalo mortality was statistically higher in outbreak areas associated with isolates from population I (13.6%) than with isolates from population II (6.9%) (p=0.047). The present study has highlighted the utility of microsatellite loci to improve understanding of the epidemiology of T. evansi and in tracking surra outbreaks.
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Affiliation(s)
- L M McInnes
- Division of Health Sciences, School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Perth, WA 6150, Australia.
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Bevivino A, Costa B, Cantale C, Cesarini S, Chiarini L, Tabacchioni S, Caballero-Mellado J, Dalmastri C. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC) populations belonging to Burkholderia cenocepacia IIIB and BCC6 group. BMC Microbiol 2011; 11:228. [PMID: 21995705 PMCID: PMC3377929 DOI: 10.1186/1471-2180-11-228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background A close association between maize roots and Burkholderia cepacia complex (BCC) bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT) the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico), in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs), respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types) analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94%) were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA). The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within each local microbial population, favouring the spread of a single clone above the rest of the recombinant population.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development) Casaccia Research Center-Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 S, Maria di Galeria, Rome, Italy.
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Schubert K, Groenewald JZ, Braun U, Dijksterhuis J, Starink M, Hill CF, Zalar P, de Hoog GS, Crous PW. Biodiversity in the Cladosporium herbarum complex (Davidiellaceae, Capnodiales), with standardisation of methods for Cladosporium taxonomy and diagnostics. Stud Mycol 2011; 58:105-56. [PMID: 18490998 PMCID: PMC2104742 DOI: 10.3114/sim.2007.58.05] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The Cladosporium herbarum complex comprises five species for which Davidiella teleomorphs are known. Cladosporium herbarum s. str. (D. tassiana), C. macrocarpum (D. macrocarpa) and C. bruhnei (D. allicina) are distinguishable by having conidia of different width, and by teleomorph characters. Davidiella variabile is introduced as teleomorph of C. variabile, a homothallic species occurring on Spinacia, and D. macrospora is known to be the teleomorph of C. iridis on Iris spp. The C. herbarum complex combines low molecular distance with a high degree of clonal or inbreeding diversity. Entities differ from each other by multilocus sequence data and by phenetic differences, and thus can be interpreted to represent individual taxa. Isolates of the C. herbarum complex that were formerly associated with opportunistic human infections, cluster with C. bruhnei. Several species are newly described from hypersaline water, namely C. ramotenellum, C. tenellum, C. subinflatum, and C. herbaroides. Cladosporium pseudiridis collected from Iris sp. in New Zealand, is also a member of this species complex and shown to be distinct from C. iridis that occurs on this host elsewhere in the world. A further new species from New Zealand is C. sinuosum on Fuchsia excorticata. Cladosporium antarcticum is newly described from a lichen, Caloplaca regalis, collected in Antarctica, and C. subtilissimum from grape berries in the U.S.A., while the new combination C. ossifragi, the oldest valid name of the Cladosporium known from Narthecium in Europe, is proposed. Standard protocols and media are herewith proposed to facilitate future morphological examination of Cladosporium spp. in culture, and neotypes or epitypes are proposed for all species treated.
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Affiliation(s)
- K Schubert
- Botanische Staatssammlung München, Menzinger Strasse 67, D-80638 München, Germany
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Do T, Gilbert S, Klein J, Warren S, Wade W, Beighton D. Clonal structure of Streptococcus sanguinis strains isolated from endocarditis cases and the oral cavity. Mol Oral Microbiol 2011; 26:291-302. [DOI: 10.1111/j.2041-1014.2011.00618.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Dixit J, Srivastava H, Singh O, Saksena D, Das A. Multilocus nuclear DNA markers and genetic parameters in an Indian Anopheles minimus population. INFECTION GENETICS AND EVOLUTION 2011; 11:572-9. [DOI: 10.1016/j.meegid.2011.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 01/03/2011] [Accepted: 01/06/2011] [Indexed: 01/26/2023]
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Weir W, Karagenç T, Gharbi M, Simuunza M, Aypak S, Aysul N, Darghouth MA, Shiels B, Tait A. Population diversity and multiplicity of infection in Theileria annulata. Int J Parasitol 2011; 41:193-203. [PMID: 20833170 PMCID: PMC3034872 DOI: 10.1016/j.ijpara.2010.08.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/26/2010] [Accepted: 08/26/2010] [Indexed: 12/03/2022]
Abstract
The tick-borne apicomplexan parasite Theileria annulata is endemic in many sub-tropical countries and causes the bovine disease tropical theileriosis. Although the parasite is known to be highly diverse, detailed information is lacking on the genetic structure of natural populations and levels of multiplicity of infection in the cattle host. With the widespread deployment of live attenuated vaccines and the emergence of drug-resistant parasites in the field, it is vital to appreciate the factors which shape genetic diversity of the parasite both within individual hosts and in the wider population. This study addresses these issues and represents an extensive genetic analysis of T. annulata populations in two endemic countries utilising a high-throughput adaptation of a micro- and mini-satellite genotyping system. Parasite material was collected from infected cattle in defined regions of Turkey and Tunisia to allow a variety of analyses to be conducted. All animals (n=305) were found to harbour multiple parasite genotypes and only two isolates shared an identical predominant multi-locus profile. A modelling approach was used to demonstrate that host age, location and vaccination status play a measurable role in determining multiplicity of infection in an individual animal. Age was shown to positively correlate with multiplicity of infection and while positive vaccination status exerted a similar effect, it was shown to be due not simply to the presence of the immunising genotype. Importantly, no direct evidence was found for the immunising genotype spreading or recombining within the local parasite community. Genetic analysis confirmed the tentative conclusion of a previous study that the parasite population appears to be, in general, panmictic. Nevertheless, evidence supporting linkage disequilibrium and a departure from panmixia was uncovered in some localities and a number of explanations for these findings are advanced.
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Affiliation(s)
- William Weir
- University of Glasgow, College of Medical, Veterinary and Life Sciences, Garscube Campus, Bearsden Road, Glasgow G61 1QH, UK.
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Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2111205] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Recombination shapes the structure of an environmental Vibrio cholerae population. Appl Environ Microbiol 2010; 77:537-44. [PMID: 21075874 DOI: 10.1128/aem.02062-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population.
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Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates. Parasitology 2010; 137:1721-30. [DOI: 10.1017/s0031182010000533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SUMMARYWith a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.
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Multiple-locus variable-number tandem-repeat analysis of the swine dysentery pathogen, Brachyspira hyodysenteriae. J Clin Microbiol 2010; 48:2859-65. [PMID: 20554811 DOI: 10.1128/jcm.00348-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodysenteriae is limited. Progress in this area has been hampered by the lack of a low-cost, portable, and discriminatory method for strain typing. The aim of the current study was to develop and test a multiple-locus variable-number tandem-repeat analysis (MLVA) method that could be used in basic veterinary diagnostic microbiology laboratories equipped with PCR technology or in more advanced laboratories with access to capillary electrophoresis. Based on eight loci, and when performed on isolates from different farms in different countries, as well as type and reference strains, the MLVA technique developed was highly discriminatory (Hunter and Gaston discriminatory index, 0.938 [95% confidence interval, 0.9175 to 0.9584]) while retaining a high phylogenetic value. Using the technique, the species was shown to be diverse (44 MLVA types from 172 isolates and strains), although isolates were stable in herds over time. The population structure appeared to be clonal. The finding of B. hyodysenteriae MLVA type 3 in piggeries in three European countries, as well as other, related, strains in different countries, suggests that spreading of the pathogen via carrier pigs is likely. MLVA overcame drawbacks associated with previous typing techniques for B. hyodysenteriae and was a powerful method for epidemiologic and population structure studies on this important pathogenic spirochete.
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The mode of reproduction in natural populations of ascomycetous fungus, Emericella nidulans, from Israel. Genet Res (Camb) 2010; 92:83-90. [PMID: 20515512 DOI: 10.1017/s0016672310000066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The mode of reproduction of the soil ascomycetous fungus Emericella nidulans of Israeli populations was studied using 15 microsatellite (simple sequence repeats or SSR) trinucleotide markers. The study was performed in three canyons: two located in the northern part of Israel (Mount Carmel and western Upper Galilee) and one in the southern Negev desert. In each canyon, E. nidulans strains were isolated from the opposite slopes and (in the desert canyon) the valley bottom. Testing the reproductive structure of the populations indicated the presence of sexuality in the northern population and predominant clonality in the desert population. The predominantly clonal character of the desert population of E. nidulans was explained by the assumption that for relevant multilocus systems of a fungus, only several haplotypes can survive in the rather constant, extremely stressful desert conditions. Additionally, the very low density of E. nidulans populations in the soil of the desert canyon, which reduces the probability of finding a sexual partner, might favour predominant clonality via selfing. Increasing sexuality in E. nidulans populations on the north-facing slopes of the northern canyons may be a result of biotic stress (pressure of competitive fungal species), due to the more mild ecological conditions in these canyons.
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Elboutahiri N, Thami-Alami I, Udupa SM. Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco. BMC Microbiol 2010; 10:15. [PMID: 20089174 PMCID: PMC2823721 DOI: 10.1186/1471-2180-10-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 01/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco. RESULTS RsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM), water stress (-1.5 MPa), high temperature (40 degrees C) and low pH (3.5), respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn) and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline). The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P < 0.01) genetic variation was distributed within regions (89%) than among regions (11%). CONCLUSION High degree of phenotypic and genotypic diversity is present in S. meliloti and S. medicae populations from marginal soils affected by salt and drought, in arid and semi-arid regions of Morocco. Some of the tolerant strains have a potential for exploitation in salt and drought affected areas for biological nitrogen fixation in alfalfa.
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Affiliation(s)
- Nadia Elboutahiri
- Institut National de la Recherche Agronomique (INRA), Centre Régional de la Recherche Agronomique de Rabat, B,P, 415, Rabat, Morocco
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Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Price EP, Glass MB, Leadem B, Beckstrom-Sternberg JS, Allan GJ, Foster JT, Wagner DM, Okinaka RT, Sim SH, Pearson O, Wu Z, Chang J, Kaul R, Hoffmaster AR, Brettin TS, Robison RA, Mayo M, Gee JE, Tan P, Currie BJ, Keim P. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 2009; 7:78. [PMID: 19922616 PMCID: PMC2784454 DOI: 10.1186/1741-7007-7-78] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 11/18/2009] [Indexed: 12/02/2022] Open
Abstract
Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.
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Affiliation(s)
- Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
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Ko KS, Kuwahara T, Lee K, Kook YH. Population structure and distribution of virulence-related genes of Bacteroides fragilis isolates from Korea and Japan. Diagn Microbiol Infect Dis 2009; 64:340-3. [DOI: 10.1016/j.diagmicrobio.2009.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/13/2009] [Accepted: 03/13/2009] [Indexed: 10/20/2022]
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ALPERMANN TILMANJ, BESZTERI BÁNK, JOHN UWE, TILLMANN URBAN, CEMBELLA ALLAND. Implications of life-history transitions on the population genetic structure of the toxigenic marine dinoflagellateAlexandrium tamarense. Mol Ecol 2009; 18:2122-33. [DOI: 10.1111/j.1365-294x.2009.04165.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Larios-Sanz M, Travisano M. Experimental evolution of an essential Bacillus gene in an E. coli host. Methods Mol Biol 2009; 532:269-287. [PMID: 19271191 DOI: 10.1007/978-1-60327-853-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The acquisition of foreign genes by HGT potentially greatly speeds up adaptation by allowing faster evolution of beneficial traits. The evolutionary integration of novel genes into host gene expression and physiology is critical for adaptation by HGT, but remains largely unknown. We are exploring the evolutionary consequences of gene acquisition in populations of Escherichia coli in real time. A plasmid bearing the genes necessary for sucrose catabolism was constructed and introduced into a single E. coli genotype. Wild-type E. coli is generally incapable of utilizing sucrose, but E. coli transformants were able to grow on sucrose as a sole carbon and energy source, albeit poorly. Twelve replicate populations were initiated and propagated in sucrose minimal media for 300 generations. Over this time, we observed large fitness improvements in the selected environment. These results demonstrate the potential for HGT to substantially increase microbial niche breadth.
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Affiliation(s)
- Maia Larios-Sanz
- Department of Biology, University of St. Thomas, Houston, TX, USA
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Karchani-Balma S, Gautier A, Raies A, Fournier E. Geography, plants, and growing systems shape the genetic structure of Tunisian Botrytis cinerea populations. PHYTOPATHOLOGY 2008; 98:1271-1279. [PMID: 19000001 DOI: 10.1094/phyto-98-12-1271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Botrytis cinerea, considered for a long time as a generalist fungal pathogen of a multitude of plants, was recently shown to exhibit significant population structure in France according to the host, suggesting sympatric specialization. Recent models also showed that adaptation to new hosts may facilitate the process of sympatric speciation in fungal plant pathogens. The present work aimed at investigating if host plants, combined with geographic origin and growing systems, shape the diversity and structure of Tunisian populations of B. cinerea. We genotyped 153 isolates with 9 microsatellites. In all the investigated populations, the fungus reproduced mainly sexually. Gene flow was significantly reduced between greenhouses and open fields from strawberry but not from grapevine. Populations from tomatoes, sampled under greenhouses only, exhibited a low genotypic diversity. The effects of plant and geography from open fields were investigated on a sample of 74 isolates. Six populations were inferred, mainly structured according to a geographic barrier corresponding to the Grande Dorsale Mountain. However, this effect could not be separated from the host plant origin of isolates. The analysis of 63 isolates recovered from strawberries and faba beans in the Cap Bon and Centre regions did not reveal any significant effect of plant on pathogen population differentiation.
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Affiliation(s)
- S Karchani-Balma
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, Tunisie
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