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Abuelmaali SA, Mashlawi AM, Ishak IH, Wajidi MFF, Jaal Z, Avicor SW, Kassim NFA. Population genetic structure of Aedes aegypti subspecies in selected geographical locations in Sudan. Sci Rep 2024; 14:2978. [PMID: 38316804 PMCID: PMC10844603 DOI: 10.1038/s41598-024-52591-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024] Open
Abstract
Although knowledge of the composition and genetic diversity of disease vectors is important for their management, this is limiting in many instances. In this study, the population structure and phylogenetic relationship of the two Aedes aegypti subspecies namely Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf) in eight geographical areas in Sudan were analyzed using seven microsatellite markers. Hardy-Weinberg Equilibrium (HWE) for the two subspecies revealed that Aaa deviated from HWE among the seven microsatellite loci, while Aaf exhibited departure in five loci and no departure in two loci (A10 and M201). The Factorial Correspondence Analysis (FCA) plots revealed that the Aaa populations from Port Sudan, Tokar, and Kassala clustered together (which is consistent with the unrooted phylogenetic tree), Aaf from Fasher and Nyala populations clustered together, and Gezira, Kadugli, and Junaynah populations also clustered together. The Bayesian cluster analysis structured the populations into two groups suggesting two genetically distinct groups (subspecies). Isolation by distance test revealed a moderate to strong significant correlation between geographical distance and genetic variations (p = 0.003, r = 0.391). The migration network created using divMigrate demonstrated that migration and gene exchange between subspecies populations appear to occur based on their geographical proximity. The genetic structure of the Ae. aegypti subspecies population and the gene flow among them, which may be interpreted as the mosquito vector's capacity for dispersal, were revealed in this study. These findings will help in the improvement of dengue epidemiology research including information on the identity of the target vector/subspecies and the arboviruses vector surveillance program.
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Affiliation(s)
- Sara A Abuelmaali
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, 11115, Sudan
| | - Abadi M Mashlawi
- Department of Biology, College of Science, Jazan University, P.O. Box. 114, Jazan, 45142, Kingdom of Saudi Arabia
| | - Intan Haslina Ishak
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | | | - Zairi Jaal
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Silas Wintuma Avicor
- Molecular Entomology Research Group, Universiti Sains Malaysia, 11800, Penang, Malaysia
- Entomology Division, Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | - Nur Faeza Abu Kassim
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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García-Meseguer AJ, Villastrigo A, Mirón-Gatón JM, Millán A, Velasco J, Muñoz I. Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes on Ochthebius Beetles from Supratidal Rockpools. INSECTS 2023; 14:881. [PMID: 37999080 PMCID: PMC10672297 DOI: 10.3390/insects14110881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools.
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Affiliation(s)
| | - Adrián Villastrigo
- Division of Entomology, SNSB-Zoologische Staatssammlung München, 81247 Munich, Germany;
| | - Juana María Mirón-Gatón
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Andrés Millán
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Josefa Velasco
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Irene Muñoz
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040 Madrid, Spain;
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Mahalle RM, Bosamia TC, Chakravarty S, Srivastava K, Meena RS, Kadam US, Srivastava CP. De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer. Genes (Basel) 2023; 14:1433. [PMID: 37510337 PMCID: PMC10379186 DOI: 10.3390/genes14071433] [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: 05/08/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.
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Affiliation(s)
- Rashmi Manohar Mahalle
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tejas C Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Snehel Chakravarty
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Kartikeya Srivastava
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Radhe S Meena
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chandra P Srivastava
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
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Large-scale genetic admixture suggests high dispersal in an insect pest, the apple fruit moth. PLoS One 2020; 15:e0236509. [PMID: 32785243 PMCID: PMC7423104 DOI: 10.1371/journal.pone.0236509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 11/25/2022] Open
Abstract
Knowledge about population genetic structure and dispersal capabilities is important for the development of targeted management strategies for agricultural pest species. The apple fruit moth, Argyresthia conjugella (Lepidoptera, Yponomeutidae), is a pre-dispersal seed predator. Larvae feed on rowanberries (Sorbus aucuparia), and when rowanberry seed production is low (i.e., inter-masting), the moth switches from laying eggs in rowanberries to apples (Malus domestica), resulting in devastating losses in apple crops. Using genetic methods, we investigated if this small moth expresses any local genetic structure, or alternatively if gene flow may be high within the Scandinavian Peninsula (~850.000 km2, 55o - 69o N). Genetic diversity was found to be high (n = 669, mean He = 0.71). For three out of ten tetranucleotide STRs, we detected heterozygote deficiency caused by null alleles, but tests showed little impact on the overall results. Genetic differentiation between the 28 sampling locations was very low (average FST = 0.016, P < 0.000). Surprisingly, we found that all individuals could be assigned to one of two non-geographic genetic clusters, and that a third, geographic cluster was found to be associated with 30% of the sampling locations, with weak but significant signals of isolation-by-distance. Conclusively, our findings suggest wind-aided dispersal and spatial synchrony of both sexes of the apple fruit moth over large areas and across very different climatic zones. We speculate that the species may recently have had two separate genetic origins caused by a genetic bottleneck after inter-masting, followed by rapid dispersal and homogenization of the gene pool across the landscape. We suggest further investigations of spatial genetic similarities and differences of the apple fruit moth at larger geographical scales, through life-stages, across inter-masting, and during attacks by the parasitoid wasp (Microgaster politus).
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Fabres AA, Valladares MA, Sáez PA, Collado GA, Pastenes L, Méndez MA. Novel microsatellite markers for an endangered freshwater snail, Heleobia atacamensis (Caenogastropoda: Cochliopidae), from the Atacama Saltpan. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1775367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Alejandra A. Fabres
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile. Las Palmeras 3425, Santiago, Chile
| | - Moisés A. Valladares
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile. Las Palmeras 3425, Santiago, Chile
| | - Paola A. Sáez
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile. Las Palmeras 3425, Santiago, Chile
| | - Gonzalo A. Collado
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío. Av. Andrés Bello 720, Chillán, Chile
| | - Luis Pastenes
- Laboratorio de Genética y Adaptación a Ambientes Extremos, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule. Av. San Miguel #3605, Talca, Chile
| | - Marco A. Méndez
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile. Las Palmeras 3425, Santiago, Chile
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Trochez-Solarte JD, Ruiz-Erazo X, Almanza-Pinzon M, Zambrano-Gonzalez G. Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review. F1000Res 2019; 8:1424. [PMID: 32148760 PMCID: PMC7043130 DOI: 10.12688/f1000research.20052.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 11/23/2022] Open
Abstract
In the genome of
Bombyx mori Linnaeus (1758), the microsatellites, or simple sequence repeats (SSR), feature among their particular characteristics a high adenine and thymine (A/T) content, low number of repeats, low frequency, and a grouping in "families" with similar flanking regions. Such characteristics may be the result of a complex interaction between factors that limit the size and dispersion of SSR loci—such as their high association with transposons—and mean that microsatellites within this taxon suitable as molecular markers are relatively rare. The determination of genetic profiles in populations and cell lines has not been affected owing to the high level of polymorphism, nor has the analysis of diversity, structure and genetic relationships. However, the scarcity of suitable microsatellites has restricted their application in genetic mapping, limiting them to preliminary identification of gene location of genes or quantitative trait loci (QTLs) related to thermotolerance, resistance to viruses, pigmentation patterns, body development and the weight of the cocoon, the cortex, the pupa and the filament. The review confirms that, as markers, microsatellites are versatile and perform well. They could thus be useful both to advance research in emerging countries with few resources seeking to promote sericulture in their territories, and to advance in the genetic and molecular knowledge of characteristics of productive and biological interest, given the latest technological developments in terms of the sequencing, identification, isolation and genotyping of SSR loci.
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Affiliation(s)
- Julian David Trochez-Solarte
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Ximena Ruiz-Erazo
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Martha Almanza-Pinzon
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Giselle Zambrano-Gonzalez
- Biology Department, Geology, Ecology and Conservation Research Group (GECO), Faculty of Natural Sciences and Education, University of Cauca, Popayán, Cauca, 190002, Colombia
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Development of novel microsatellites for population genetic analysis of Phenacoccus solenopsis Tinsley (Hemipeta: Pseudoccoccidae) based on genomic analysis. Int J Biol Macromol 2018; 121:1135-1144. [PMID: 30352227 DOI: 10.1016/j.ijbiomac.2018.10.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/13/2018] [Accepted: 10/18/2018] [Indexed: 01/17/2023]
Abstract
The cotton mealybug, Phenacoccus solenopsis Tinsley (Hemipeta: Pseudoccoccidae), is an aggressively invasive pest causing huge economic losses of crops around the world. In this study, we developed genome-wide microsatellites for population genetic analysis of P. solenopsis. We obtained a random genome of P. solenopsis with a size of 267.07 Mb and scaffold N50 of 14.12 Kb. In total 115,639 microsatellites were isolated from the genome, of which those with trinucleotide motifs were the most abundant. Forty-two polymorphic loci were selected for primer validation based on three populations. Allele numbers varied from 2 to 5 with an average value of 2.5 per locus, and allelic richness ranged from 1.00 to 4.48. The observed heterozygosity (H0) and expected heterozygosity (HE) ranged from 0.00 to 0.92 and 0.00 to 0.73, respectively. Population genetic structure analysis based on the developed markers revealed strong differentiation between three populations of P. solenopsis collected from its invasive range in China. The microsatellites developed in our study should provide efficient genetic markers for population level studies of P. solenopsis to reveal invasion history and patterns of dispersal.
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Fu Z, Epstein B, Kelley JL, Zheng Q, Bergland AO, Castillo Carrillo CI, Jensen AS, Dahan J, Karasev AV, Snyder WE. Using NextRAD sequencing to infer movement of herbivores among host plants. PLoS One 2017; 12:e0177742. [PMID: 28505182 PMCID: PMC5432177 DOI: 10.1371/journal.pone.0177742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 05/02/2017] [Indexed: 12/29/2022] Open
Abstract
Herbivores often move among spatially interspersed host plants, tracking high-quality resources through space and time. This dispersal is of particular interest for vectors of plant pathogens. Existing molecular tools to track such movement have yielded important insights, but often provide insufficient genetic resolution to infer spread at finer spatiotemporal scales. Here, we explore the use of Nextera-tagmented reductively-amplified DNA (NextRAD) sequencing to infer movement of a highly-mobile winged insect, the potato psyllid (Bactericera cockerelli), among host plants. The psyllid vectors the pathogen that causes zebra chip disease in potato (Solanum tuberosum), but understanding and managing the spread of this pathogen is limited by uncertainty about the insect's host plant(s) outside of the growing season. We identified 1,978 polymorphic loci among psyllids separated spatiotemporally on potato or in patches of bittersweet nightshade (S. dulcumara), a weedy plant proposed to be the source of potato-colonizing psyllids. A subset of the psyllids on potato exhibited genetic similarity to insects on nightshade, consistent with regular movement between these two host plants. However, a second subset of potato-collected psyllids was genetically distinct from those collected on bittersweet nightshade; this suggests that a currently unrecognized source, i.e., other nightshade patches or a third host-plant species, could be contributing to psyllid populations in potato. Oftentimes, dispersal of vectors of pathogens must be tracked at a fine scale in order to understand, predict, and manage disease spread. We demonstrate that emerging sequencing technologies that detect genome-wide SNPs of a vector can be used to infer such localized movement.
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Affiliation(s)
- Zhen Fu
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Qi Zheng
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
| | - Alan O. Bergland
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Andrew S. Jensen
- Northwest Potato Research Consortium, Lakeview, Oregon, United States of America
| | - Jennifer Dahan
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Alexander V. Karasev
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - William E. Snyder
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
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Ke F, You S, He W, Liu T, Vasseur L, Douglas CJ, You M. Genetic differentiation of the regional Plutella xylostella populations across the Taiwan Strait based on identification of microsatellite markers. Ecol Evol 2015; 5:5880-91. [PMID: 26811762 PMCID: PMC4717340 DOI: 10.1002/ece3.1850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022] Open
Abstract
Movement of individuals through events, such as storms or crop transportation, may affect survival and distribution of insect pests, as well as population genetic structure at a regional scale. Understanding what factors contribute to gene flow in pest populations remains very important for sustainable pest management. The diamondback moth (Plutella xylostella) is an insect pest well known for its capacity of moving over short to long distances. Here, we used newly isolated microsatellite markers to analyze the genetic structure of nine populations across the Taiwan Strait of China (Taiwan and Fujian). A total of 12,152 simple sequence repeats (SSRs) were initially identified from the P. xylostella transcriptome (~94 Mb), with an average of 129 SSRs per Mb. Nine SSRs were validated to be polymorphic markers, and eight were used for this population genetic study. Our results showed that the P. xylostella populations could be divided into distinct two clusters, which is likely due to the year-round airflows in this region. A pattern of isolation by distance among the local populations within Fujian was found, and may be related to vegetable transportation. Considering the complexity of the P. xylostella population genetic structure from local and regional to global levels, we propose that developing ecologically sound strategies for managing this pest will require knowledge of the link between behavioral and population ecology and its genetic structure.
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Affiliation(s)
- Fushi Ke
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Shijun You
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of BotanyUniversity of British Columbia#3529‐6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Weiyi He
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Tiansheng Liu
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
| | - Liette Vasseur
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of Biological SciencesBrock University500 Glenridge AvenueSt. CatharinesOntarioL2S 3A1Canada
| | - Carl J. Douglas
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Department of BotanyUniversity of British Columbia#3529‐6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Minsheng You
- Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou350002China
- Fujian‐Taiwan Joint Innovative Centre for Ecological Control of Crop PestsFujian Agriculture and Forestry UniversityFuzhou350002China
- Key Laboratory of Integrated Pest Management for Fujian‐Taiwan CropsMinistry of AgricultureFuzhou350002China
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Characterization of microsatellites and repetitive flanking sequences (ReFS) from the topmouth culter (Culter alburnus Basilewsky). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations. Sci Rep 2015; 5:15728. [PMID: 26510465 PMCID: PMC4625160 DOI: 10.1038/srep15728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/30/2015] [Indexed: 11/08/2022] Open
Abstract
Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (FST = 0.154) and considerable inbreeding (FIS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology.
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Reineke A, Assaf HA, Kulanek D, Mori N, Pozzebon A, Duso C. A novel set of microsatellite markers for the European Grapevine Moth Lobesia botrana isolated using next-generation sequencing and their utility for genetic characterization of populations from Europe and the Middle East. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:408-416. [PMID: 25850369 DOI: 10.1017/s0007485315000267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Using a high-throughput 454 pyrosequencing approach a novel set of microsatellite markers was developed for one of the key grapevine insect pests, the European grapevine moth Lobesia botrana (Lepidoptera: Tortricidae). 20 primer pairs flanking a microsatellite motif were designed based on the sequences obtained and were subsequently evaluated in a sample of 14 L. botrana populations from Europe and the Middle East. 11 markers showed stable and reproducible amplification patterns; however, one of the 11 markers was monomorphic in all L. botrana populations analysed. Estimated frequencies of null alleles of more than 20% were evident for two of the markers tested, but varied substantially depending on the respective L. botrana population. In 12 of the 14 L. botrana populations observed heterozygosities were lower to those expected under Hardy-Weinberg equilibrium, indicating a deficiency of heterozygotes in the respective populations. The overall F ST value of 0.075 suggested a moderate but significant genetic differentiation between the L. botrana populations included in this study. In addition, a clear geographic structure was detected in the set of samples, evident through a significant isolation by distance and through results from structure analysis. In structure analysis, L. botrana populations were grouped in two clearly separated clusters according to their European (Spain, Italy, Germany) or Middle Eastern (Israel, Syria, Turkey) origin. This novel set of microsatellite markers can now be applied to study the evolutionary ecology of this species including host shifts and host adaptation as well as spread of individuals across worldwide viticulture.
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Affiliation(s)
- A Reineke
- Department of Phytomedicine,Geisenheim University,D-65366 Geisenheim,Germany
| | - H A Assaf
- Department of Phytomedicine,Geisenheim University,D-65366 Geisenheim,Germany
| | - D Kulanek
- Department of Phytomedicine,Geisenheim University,D-65366 Geisenheim,Germany
| | - N Mori
- Department of Agronomy, Food, Natural Resources, Animals and the Environment,University of Padova,35020 Legnaro (Padova),Italy
| | - A Pozzebon
- Department of Agronomy, Food, Natural Resources, Animals and the Environment,University of Padova,35020 Legnaro (Padova),Italy
| | - C Duso
- Department of Agronomy, Food, Natural Resources, Animals and the Environment,University of Padova,35020 Legnaro (Padova),Italy
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Caplins SA, Gilbert KJ, Ciotir C, Roland J, Matter SF, Keyghobadi N. Landscape structure and the genetic effects of a population collapse. Proc Biol Sci 2015; 281:20141798. [PMID: 25320176 DOI: 10.1098/rspb.2014.1798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60-100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.
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Affiliation(s)
- Serena A Caplins
- Center for Population Biology, Department of Evolution and Ecology, College of Biological Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Kimberly J Gilbert
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Claudia Ciotir
- Department of Environmental Life Sciences, Trent University, Peterborough, Ontario, Canada K9J 7B8
| | - Jens Roland
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 445221, USA
| | - Nusha Keyghobadi
- Department of Biology, Western University, 1151 Richmond St., North, London, Ontario, Canada N6A 5B7
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Nam HY, Coates B, Kim KS, Park M, Lee JH. Characterization of 12 Novel Microsatellite Markers of Sogatella furcifera (Hemiptera: Delphacidae) Identified From Next-Generation Sequence Data. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev069. [PMID: 26163593 PMCID: PMC4535569 DOI: 10.1093/jisesa/iev069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a major pest of rice and has long-range migratory behavior in Asia. Microsatellite markers (simple sequence repeats) have been widely used to determine the origins and genetic diversity of insect pests. We identified novel microsatellite loci for S. furcifera samples collected from Laos, Vietnam, and three localities in Bangladesh from next-generation Roche 454 pyrosequencing data. Size polymorphism at 12 microsatellite loci was verified for 40 adult individuals collected from Shinan, South Korea. The average number of alleles per locus was 7.92. The mean values of observed (H(o)) and expected heterozygosities (H(E)) were 0.615 and 0.757, respectively. These new microsatellite markers will be a resource for future ecological genetic studies of S. furcifera samples across more broad geographic regions in Asia and may assist in estimations of genetic differentiation and gene flow among populations for implementation of more effective management strategies to control this serious rice pest.
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Affiliation(s)
- Hwa Yeun Nam
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Brad Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 113 Genetics Laboratory, Iowa State University, Ames, IA 50011
| | - Kyung Seok Kim
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 113 Genetics Laboratory, Iowa State University, Ames, IA 50011
| | - Marana Park
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Joon-Ho Lee
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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15
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Cao LJ, Wen JB, Wei SJ, Liu J, Yang F, Chen M. Characterization of novel microsatellite markers for Hyphantria cunea and implications for other Lepidoptera. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:273-284. [PMID: 25772405 DOI: 10.1017/s0007485315000061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers for H. cunea from SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified as Grouped should not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy-Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, and F ST performed better than did R ST for the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies of H. cunea.
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Affiliation(s)
- L J Cao
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - J B Wen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - S J Wei
- Institute of Plant and Environmental Protection,Beijing Academy of Agriculture and Forestry Sciences,Beijing 100097,China
| | - J Liu
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - F Yang
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - M Chen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
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MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula. Genetica 2015; 143:433-40. [PMID: 25981486 PMCID: PMC4486113 DOI: 10.1007/s10709-015-9842-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/10/2015] [Indexed: 12/31/2022]
Abstract
Transposable elements (TEs) are mobile DNA segments, abundant and dynamic in plant genomes. Because their mobility can be potentially deleterious to the host, a variety of mechanisms evolved limiting that negative impact, one of them being preference for a specific target insertion site. Here, we describe a family of Mutator-like DNA transposons in Medicago truncatula targeting TA microsatellites. We identified 218 copies of MuTAnTs and an element carrying a complete ORF encoding a mudrA-like transposase. Most insertion sites are flanked by a variable number of TA tandem repeats, indicating that MuTAnTs are specifically targeting TA microsatellites. Other TE families flanked by TA repeats (e.g. TAFT elements in maize) were described previously, however we identified the first putative autonomous element sharing that characteristics with a related group of short non-autonomous transposons.
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Addamo AM, García-Jiménez R, Taviani M, Machordom A. Development of Microsatellite Markers in the Deep-Sea Cup Coral Desmophyllum dianthus by 454 Sequencing and Cross-Species Amplifications in Scleractinia Order. J Hered 2015; 106:322-30. [PMID: 25810120 DOI: 10.1093/jhered/esv010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 02/16/2015] [Indexed: 11/12/2022] Open
Abstract
Microsatellite loci were isolated for the first time for the deep-sea coral Desmophyllum dianthus, using 454 GS-FLX Titanium pyrosequencing. We developed conditions for amplifying 24 markers in 10 multiplex reactions. Three to 16 alleles per locus were detected across 25 samples analyzed from Santa Maria di Leuca coral province (Mediterranean Sea). For the 24 polymorphic loci, observed and expected heterozygosities ranged from 0.211 to 0.880 and 0.383 to 0.910, respectively; 3 loci deviated from Hardy-Weinberg equilibrium, after null allele and sequential Holm-Bonferroni corrections. These newly isolated microsatellites are very useful genetic markers that provide data for future conservation strategies. Cross-amplification of these microsatellites, tested in 46 coral species, representing 40 genera, and 10 families of the phylum Cnidaria, produced informative allelic profiles for 1 to 24 loci. The utility of extending analyses to cross-species amplifications is also discussed.
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Affiliation(s)
- Anna M Addamo
- From the Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain (Addamo, García-Jiménez, and Machordom); and the Istituto di Scienze Marine-CNR, Bologna, Italy (Taviani).
| | - Ricardo García-Jiménez
- From the Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain (Addamo, García-Jiménez, and Machordom); and the Istituto di Scienze Marine-CNR, Bologna, Italy (Taviani)
| | - Marco Taviani
- From the Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain (Addamo, García-Jiménez, and Machordom); and the Istituto di Scienze Marine-CNR, Bologna, Italy (Taviani)
| | - Annie Machordom
- From the Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain (Addamo, García-Jiménez, and Machordom); and the Istituto di Scienze Marine-CNR, Bologna, Italy (Taviani)
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18
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White VL, Endersby NM, Chan J, Hoffmann AA, Weeks AR. Developing Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in three Aedes disease vectors. INSECT SCIENCE 2015; 22:409-423. [PMID: 24895297 DOI: 10.1111/1744-7917.12145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/25/2014] [Indexed: 06/03/2023]
Abstract
Aedes aegypti, Aedes notoscriptus, and Aedes albopictus are important vectors of many arboviruses implicated in human disease such as dengue fever. Genetic markers applied across vector species can provide important information on population structure, gene flow, insecticide resistance, and taxonomy, however, robust microsatellite markers have proven difficult to develop in these species and mosquitoes generally. Here we consider the utility and transferability of 15 Ribosome protein (Rp) Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in these 3 Aedes species. Rp EPIC markers designed for Ae. aegypti also successfully amplified populations of the sister species, Ae. albopictus, as well as the distantly related species, Ae. notoscriptus. High SNP and good indel diversity in sequenced alleles plus support for amplification of the same regions across populations and species were additional benefits of these markers. These findings point to the general value of EPIC markers in mosquito population studies.
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Affiliation(s)
- Vanessa Linley White
- Department of Genetics, Bio21 Institute, the University of Melbourne, Victoria, 3010, Australia
| | - Nancy Margaret Endersby
- Department of Genetics, Bio21 Institute, the University of Melbourne, Victoria, 3010, Australia
| | - Janice Chan
- Department of Genetics, Bio21 Institute, the University of Melbourne, Victoria, 3010, Australia
| | - Ary Anthony Hoffmann
- Department of Genetics, Bio21 Institute, the University of Melbourne, Victoria, 3010, Australia
| | - Andrew Raymond Weeks
- Department of Genetics, Bio21 Institute, the University of Melbourne, Victoria, 3010, Australia
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Minter EJA, Lowe CD, Brockhurst MA, Watts PC. A rapid and cost‐effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ewan J. A. Minter
- Department of Biology University of York Wentworth Way York Yorkshire YO10 5DD UK
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
| | - Chris D. Lowe
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
- Centre for Ecology and Conservation College of Life and Environmental Sciences University of Exeter Cornwall Campus Falmouth TR10 9FE UK
| | | | - Phillip C. Watts
- Institute of Integrative Biology University of Liverpool Biosciences Building Crown Street Liverpool L69 7ZB UK
- Department of Biology University of Oulu PO Box 3000 FI‐90014 Oulu Finland
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20
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Li J, Coates BS, Kim KS, Bourguet D, Ponsard S, He K, Wang Z. The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize. J Hered 2014; 105:642-55. [PMID: 25024271 DOI: 10.1093/jhered/esu036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance indicated that geographic region, number of generations or voltinism accounted for <0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified 4 distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal component analyses, which showed significant differentiation with multivoltine populations (φST=0.400; P value<0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.
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Affiliation(s)
- Jing Li
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Brad S Coates
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Kyung Seok Kim
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Denis Bourguet
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Sergine Ponsard
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Kanglai He
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard)
| | - Zhenying Wang
- From the State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China (Li, He, and Wang); the School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province, China (Li); the United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA (Coates and Kim); the Centre de Biologie pour la Gestion des Populations (CBGP) UMR INRA-IRD-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France (Bourguet); the Université Toulouse 3 Paul Sabatier, Centre National de la Recherche Scientifique, ENFA, UMR5174 EDB (Laboratoire Evolution and Diversité Biologique), Toulouse, France (Ponsard); and the Centre National de la Recherche Scientifique, Université Paul Sabatier, UMR5174 EDB, Toulouse, France (Ponsard).
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21
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Nantón A, Arias-Pérez A, Méndez J, Freire R. Characterization of nineteen microsatellite markers and development of multiplex PCRs for the wedge clam Donax trunculus (Mollusca: Bivalvia). Mol Biol Rep 2014; 41:5351-7. [PMID: 24852303 DOI: 10.1007/s11033-014-3406-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/09/2014] [Indexed: 12/01/2022]
Abstract
The wedge clam Donax trunculus is an Atlantic-Mediterranean warm-temperate species found from Senegal to the northern coast of France, including the Mediterranean and Black Sea. It is commercially exploited in several European countries and constitutes an important fishing resource due to its high economical value. To contribute to its conservation and management, nineteen microsatellite markers were isolated from two enriched genomic libraries. These loci were characterized in 30 clams from a single population from northwest Spain. The number of alleles per locus ranged from 2 to 17 and observed and expected heterozygosity varied from zero to 0.714 and from 0.078 to 0.950, respectively. Linkage disequilibrium was not detected and nine loci were in agreement with Hardy-Weinberg equilibrium. Fifteen polymorphic markers were arranged into three multiplex PCR sets to reduce both time and cost of microsatellite genotyping. This is the first time that polymorphic microsatellite markers have been reported for D. trunculus. These new markers provide a valuable resource for future population genetics studies and management and culture of this species.
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Affiliation(s)
- Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071 A Coruña, Spain,
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22
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Correa MCG, Zaviezo T, Le Maguet J, Herrbach E, Malausa T. Characterization of microsatellite DNA libraries from three mealybug species and development of microsatellite markers for Pseudococcus viburni (Hemiptera: Pseudococcidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:213-220. [PMID: 24345408 DOI: 10.1017/s0007485313000667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mealybugs (Hemiptera: Pseudococcidae) are important pests for crops worldwide. Different species, cryptic taxa under the same species name or even populations within a species can differ in biological characteristics, such as phenology, resistance to insecticides, virus transmission and susceptibility to natural enemies. Therefore, their management efficacy depends on their accurate identification. Microsatellite genetic markers are efficient in revealing the fine-scale taxonomic status of insects, both at inter- and intra-specific level. Despite their potential uses, microsatellites have been developed only for one mealybug species so far. Hence, it is unclear whether microsatellites may be useful to assess mealybug population differentiation and structuring. In this work, we tested the feasibility of developing microsatellite markers in mealybugs by: (i) producing and characterizing microsatellite DNA libraries for three species: Pseudococcus viburni, Pseudococcus comstocki and Heliococcus bohemicus, and (ii) by developing and testing markers for Ps. viburni. The obtained libraries contained balanced percentages of dinucleotide (ranging from 15 to 25%) and trinucleotide (from 5 to 17%) motifs. The marker setup for Ps. viburni was successful, although 70% of the primers initially tested were discarded for a lack of polymorphism. Finally, 25 markers were combined in two multiplex polymerase chain reactions with 21 displaying no evidence of deviation from Hardy-Weinberg equilibrium. Ps. viburni markers were tested on one population from France and one from Chile. The markers revealed a significant genetic differentiation between the two populations with an Fst estimate of 0.266.
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Affiliation(s)
- M C G Correa
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
| | - T Zaviezo
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
| | - J Le Maguet
- Institut National de la Recherche Agronomique, UMR SVQV INRA/UDS, Equipe ViVe. 28, rue de Herrlisheim. BP 20507, 68000 Colmar, France
| | - E Herrbach
- Institut National de la Recherche Agronomique, UMR SVQV INRA/UDS, Equipe ViVe. 28, rue de Herrlisheim. BP 20507, 68000 Colmar, France
| | - T Malausa
- Institut National de la Recherche Agronomique, UMR ISA INRA/UNSA/CNRS, Equipe BPI. 400, route des Chappes. BP 167, 06903 Sophia-Antipolis, France
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23
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Ricci M, Luchetti A, Bonandin L, Mantovani B. Random DNA libraries from three species of the stick insect genus Bacillus (Insecta: Phasmida): repetitive DNA characterization and first observation of polyneopteran MITEs. Genome 2013; 56:729-35. [PMID: 24433208 DOI: 10.1139/gen-2013-0107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.
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Affiliation(s)
- Marco Ricci
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, via Selmi 3, 40126 Bologna, Italy
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Van Houtte N, Van Oosten AR, Jordaens K, Matthysen E, Backeljau T, Heylen DJA. Isolation and characterization of ten polymorphic microsatellite loci in Ixodes arboricola, and cross-amplification in three other Ixodes species. EXPERIMENTAL & APPLIED ACAROLOGY 2013; 61:327-336. [PMID: 23644881 DOI: 10.1007/s10493-013-9702-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
We characterized ten polymorphic microsatellite loci from the tree-hole tick, Ixodes arboricola. Loci were screened in 11-18 individuals from three Belgian populations and five to ten alleles were found at each locus. Seven loci did not show deviations from Hardy-Weinberg equilibrium conditions and there were no indications for null alleles at these loci. The three other loci showed significant heterozygote deficiencies in at least one population, and a high potential for the occurrence of null alleles. We observed no effect of potential host DNA on the scoring of the microsatellites. Cross-amplification of the microsatellites was tested in eight specimens of three congeneric species: I. ricinus, I. hexagonus and I. frontalis. Depending on the species, six or seven of the loci were amplified in ≥ 4 of the 8 specimens and were polymorphic in each of these species (except for Ixaf 11 in I. frontalis and I. ricinus). These loci thus provide a tool for population genetic analysis of I. arboricola. The suitability of these markers needs to be further investigated in its congeners.
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Affiliation(s)
- N Van Houtte
- Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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25
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Chen MH, Dorn S. Cross-amplification of microsatellites from the codling moth Cydia pomonella to three other species of the tribe Grapholitini (Lepidoptera: Tortricidae). Mol Ecol Resour 2013; 10:1034-7. [PMID: 21565113 DOI: 10.1111/j.1755-0998.2010.02837.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study examined cross-species amplification of 33 microsatellite markers, previously developed for Cydia pomonella, in three related fruit moth species of the same tribe (Grapholitini), namely Grapholita molesta, Grapholita funebrana and Grapholita lobarzewskii. Eight microsatellite loci yielded polymorphic products for G. molesta, nine for G. funebrana and 11 for G. lobarzewskii. At all these loci, the number of alleles ranged between four and 11 in G. molesta, and between four and nine in G. funebrana and G. lobarzewskii each. The successful cross-amplified loci can be used for research on population genetics and gene flow of the three target species.
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Affiliation(s)
- M H Chen
- Institute of Plant Sciences/Applied Entomology, ETH Zurich, Schmelzbergstr. 9/LFO, CH-8092 Zurich, Switzerland
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Stolle E, Kidner JH, Moritz RFA. Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera. Genome Biol Evol 2013; 5:151-62. [PMID: 23292136 PMCID: PMC3595035 DOI: 10.1093/gbe/evs133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution.
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Affiliation(s)
- Eckart Stolle
- Department of Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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27
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Habel JC, Husemann M, Schmitt T, Dapporto L, Rödder D, Vandewoestijne S. A Forest Butterfly in Sahara Desert Oases: Isolation Does Not Matter. J Hered 2012; 104:234-47. [DOI: 10.1093/jhered/ess092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Meglécz E, Nève G, Biffin E, Gardner MG. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 2012; 7:e40861. [PMID: 22815847 PMCID: PMC3397955 DOI: 10.1371/journal.pone.0040861] [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: 03/19/2012] [Accepted: 06/14/2012] [Indexed: 11/19/2022] Open
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
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Affiliation(s)
- Emese Meglécz
- IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France.
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Chapuis MP, Streiff R, Sword GA. Long microsatellites and unusually high levels of genetic diversity in the Orthoptera. INSECT MOLECULAR BIOLOGY 2012; 21:181-186. [PMID: 22211932 DOI: 10.1111/j.1365-2583.2011.01124.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Much remains to be learned about the mutational processes governing the evolution of microsatellite repeat regions and the associated levels of genetic diversity observed at microsatellite markers across populations or species. An extensive survey of microsatellite variation in 210 insect species from six major orders revealed that within Orthopterans, which are characterized by giant genomes, levels of genetic diversity were ~20% higher and microsatellite repeat arrays were longer than in any other group. Because of the mutation dependence on repeat length, this result suggests a higher microsatellite loci mutation rate in the Orthoptera. We deem it plausible that differences among insect orders, either in mismatch repair systems or in abundance of transposable element-derived microsatellites, can shape the size distribution of both genomes and microsatellite repeat regions. Our findings emphasise that observed levels of genetic diversity can greatly vary across species (orders at least) because of molecular differences in the mechanisms that determine microsatellite size, and are therefore critical to conservation and population genetics studies, where microsatellite repeat variability is primarily interpreted in terms of population demography and history.
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Rotheray EL, Greminger MP, Nater A, Krützen M, Goulson D, Bussière LF. Polymorphic microsatellite loci for the endangered pine hoverfly Blera fallax (Diptera: Syrphidae). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-011-9488-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Meglécz E, Nève G, Biffin E, Gardner MG. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 2012. [PMID: 22815847 DOI: 10.1371/journal.pone.004086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
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Affiliation(s)
- Emese Meglécz
- IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France.
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32
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Rhode C, Roodt-Wilding R. Bioinformatic survey of Haliotis midae microsatellites reveals a non-random distribution of repeat motifs. THE BIOLOGICAL BULLETIN 2011; 221:147-154. [PMID: 22042433 DOI: 10.1086/bblv221n2p147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent studies have shown the non-random distribution of microsatellite motifs between genomic regions within a particular species. This study investigates such microsatellite distributions in the genome of the economically important abalone Haliotis midae, via a bioinformatic survey. In particular, the association of specific repeat motifs to coding regions and transposable elements is investigated. An understanding of microsatellite genomic distribution will facilitate more efficient use and development of this popular molecular marker. A bias toward di- and tetranucleotide repeats was found in the H. midae genome. CA microsatellite units were the most abundant repeat motif, but were notably underrepresented in genic regions where GAGT repeats predominate. Approximately 17.5% and 21% of the microsatellites showed gene and/or transposable element associations, respectively. This could explain the high genomic frequencies of particular motifs across the genome and may allude to a possible functional role. The data presented in this study are the first to demonstrate such non-random dispersal of microsatellites in abalone and support previous findings arguing in favor of non-random distribution of repeat motifs.
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Affiliation(s)
- Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, Republic of South Africa.
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33
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Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera). CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0259-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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34
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Franck P, Ricci B, Klein EK, Olivares J, Simon S, Cornuet JM, Lavigne C. Genetic inferences about the population dynamics of codling moth females at a local scale. Genetica 2011; 139:949-60. [DOI: 10.1007/s10709-011-9598-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
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35
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Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ. Rise of the machines--recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 2011; 11:1093-101. [PMID: 21679314 DOI: 10.1111/j.1755-0998.2011.03037.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Next generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large-scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.
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Affiliation(s)
- Michael G Gardner
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
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36
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Fine-scale genetic structure of an endangered population of the Mormon metalmark butterfly (Apodemia mormo) revealed using AFLPs. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0202-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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MALAUSA THIBAUT, GILLES ANDRÉ, MEGLÉCZ EMESE, BLANQUART HÉLÈNE, DUTHOY STÉPHANIE, COSTEDOAT CAROLINE, DUBUT VINCENT, PECH NICOLAS, CASTAGNONE‐SERENO PHILIPPE, DÉLYE CHRISTOPHE, FEAU NICOLAS, FREY PASCAL, GAUTHIER PHILIPPE, GUILLEMAUD THOMAS, HAZARD LAURENT, LE CORRE VALÉRIE, LUNG‐ESCARMANT BRIGITTE, MALÉ PIERREG, FERREIRA STÉPHANIE, MARTIN JEAN. High‐throughput microsatellite isolation through 454 GS‐FLX Titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour 2011; 11:638-44. [PMID: 21676194 DOI: 10.1111/j.1755-0998.2011.02992.x] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- THIBAUT MALAUSA
- INRA, UMR 1301 IBSV INRA/UNSA/CNRS, 400 Route des Chappes, BP 167, 06903 Sophia‐Antipolis Cedex, France
| | - ANDRÉ GILLES
- Aix‐Marseille Université, CNRS, IRD, UMR 6116 – IMEP, Equipe Evolution Génome Environnement, Centre Saint‐Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
| | - EMESE MEGLÉCZ
- Aix‐Marseille Université, CNRS, IRD, UMR 6116 – IMEP, Equipe Evolution Génome Environnement, Centre Saint‐Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
| | - HÉLÈNE BLANQUART
- Genoscreen, Genomic Platform and R&D, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, Bâtiment Guérin, 59000 Lille, France
| | - STÉPHANIE DUTHOY
- Genoscreen, Genomic Platform and R&D, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, Bâtiment Guérin, 59000 Lille, France
| | - CAROLINE COSTEDOAT
- Aix‐Marseille Université, CNRS, IRD, UMR 6116 – IMEP, Equipe Evolution Génome Environnement, Centre Saint‐Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
| | - VINCENT DUBUT
- Aix‐Marseille Université, CNRS, IRD, UMR 6116 – IMEP, Equipe Evolution Génome Environnement, Centre Saint‐Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
| | - NICOLAS PECH
- Aix‐Marseille Université, CNRS, IRD, UMR 6116 – IMEP, Equipe Evolution Génome Environnement, Centre Saint‐Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France
| | | | - CHRISTOPHE DÉLYE
- INRA, UMR 1210 Biologie et Gestion des Adventices, 17 rue Sully, 21000 Dijon, France
| | - NICOLAS FEAU
- INRA, UMR 1202 BIOGECO, Equipe de Pathologie Forestière, Domaine de Pierroton, 69 route d’Arcachon, 33612 Cestas Cedex, France
| | - PASCAL FREY
- INRA, Nancy‐Université, UMR 1136, Interactions Arbres – Microorganismes, IFR 110, 54280 Champenoux, France
| | - PHILIPPE GAUTHIER
- UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
| | - THOMAS GUILLEMAUD
- INRA, UMR 1301 IBSV INRA/UNSA/CNRS, 400 Route des Chappes, BP 167, 06903 Sophia‐Antipolis Cedex, France
| | - LAURENT HAZARD
- INRA – UMR 1248 AGIR, BP 52627, 31326 Castanet‐Tolosan Cedex, France
| | - VALÉRIE LE CORRE
- INRA, UMR 1210 Biologie et Gestion des Adventices, 17 rue Sully, 21000 Dijon, France
| | - BRIGITTE LUNG‐ESCARMANT
- INRA, UMR 1202 BIOGECO, Equipe de Pathologie Forestière, Domaine de Pierroton, 69 route d’Arcachon, 33612 Cestas Cedex, France
| | - PIERRE‐JEAN G. MALÉ
- UMR Evolution et Diversité Biologique (Université Toulouse III; CNRS), 118 Route de Narbonne, 31062 Toulouse, France
| | - STÉPHANIE FERREIRA
- Genoscreen, Genomic Platform and R&D, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, Bâtiment Guérin, 59000 Lille, France
| | - JEAN‐FRANÇOIS MARTIN
- UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier‐sur‐Lez Cedex, France
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Torres-Leguizamón M, Dupas S, Dardon D, Gómez Y, Niño L, Carnero A, Padilla A, Merlin I, Fossoud A, Zeddam JL, Lery X, Capdevielle-Dulac C, Dangles O, Silvain JF. Inferring native range and invasion scenarios with mitochondrial DNA: the case of T. solanivora successive north–south step-wise introductions across Central and South America. Biol Invasions 2011. [DOI: 10.1007/s10530-010-9909-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lemer S, Rochel E, Planes S. Correction Method for Null Alleles in Species with Variable Microsatellite Flanking Regions, A Case Study of the Black-Lipped Pearl Oyster Pinctada margaritifera. J Hered 2011; 102:243-6. [DOI: 10.1093/jhered/esq123] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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40
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Sun JT, Zhang YK, Ge C, Hong XY. Mining and characterization of sequence tagged microsatellites from the brown planthopper Nilaparvata lugens. JOURNAL OF INSECT SCIENCE (ONLINE) 2011; 11:134. [PMID: 22243416 PMCID: PMC3281394 DOI: 10.1673/031.011.13401] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), is an important pest of rice. To better understand the migration pattern and population structure of the Chinese populations of N. lugens, we developed and characterized 12 polymorphic microsatellites from the expressed sequence tags database of N. lugens. The occurrence of these simple sequence repeats was assessed in three populations collected from three provinces of China. The number of alleles per locus ranged from 3 to 13 with an average of 6.5 alleles per locus. The mean observed heterozygosity of the three populations ranged from 0.051 to 0.772 and the expected heterozygosity ranged from 0.074 to 0.766. The sequences of the 12 markers were highly variable. The polymorphism information content of the 12 markers was high and ranged from 0.074 to 0.807 (mean = 0.503). Sequencing of microsatellite alleles revealed that the fragment length differences were mainly due to the variation of the repeat motif. Significant genetic differentiation was detected among the three N. lugens populations as the Fst ranged from 0.034 to 0.273. Principle coordinates analysis also revealed significant genetic differentiation between populations of different years. We conclude that these microsatellite markers will be a powerful tools to study the migration routine of the N. lugens.
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Affiliation(s)
- Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yan-Kai Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Cheng Ge
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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López-Flores I, Ruiz-Rejón C, Cross I, Rebordinos L, Robles F, Navajas-Pérez R, de la Herrán R. Molecular characterization and evolution of an interspersed repetitive DNA family of oysters. Genetica 2010; 138:1211-9. [PMID: 21072565 DOI: 10.1007/s10709-010-9517-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
Abstract
When genomic DNA from the European flat oyster Ostrea edulis L. was digested by BclI enzyme, a band of about 150 bp was observed in agarose gel. After cloning and sequencing this band and analysing their molecular characteristics and genomic organization by means of Southern blot, in situ hybridisation, and polymerase chain reaction (PCR) protocols, we concluded that this band is an interspersed highly repeated DNA element, which is related in sequence to the flanking regions of (CT)-microsatellite loci of the species O. edulis and Crassostrea gigas. Furthermore, we determined that this element forms part of a longer repetitive unit of 268 bp in length that, at least in some loci, is present in more than one copy. By Southern blot hybridisation and PCR amplifications-using primers designed for conserved regions of the 150-bp BclI clones of O. edulis-we determined that this repetitive DNA family is conserved in five other oyster species (O. stentina, C. angulata, C. gigas, C. ariakensis, and C. sikamea) while it is apparently absent in C. gasar. Finally, based on the analysis of the repetitive units in these oyster species, we discuss the slow degree of concerted evolution in this interspersed repetitive DNA family and its use for phylogenetic analysis.
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Affiliation(s)
- Inmaculada López-Flores
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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Castagnone-Sereno P, Danchin EGJ, Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics 2010; 11:598. [PMID: 20973953 PMCID: PMC3091743 DOI: 10.1186/1471-2164-11-598] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/25/2010] [Indexed: 11/13/2022] Open
Abstract
Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. Results Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)n, (AG)n and (CT)n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)n and (ATT)n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite.
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Martin JF, Pech N, Meglécz E, Ferreira S, Costedoat C, Dubut V, Malausa T, Gilles A. Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing. BMC Genomics 2010; 11:560. [PMID: 20939885 PMCID: PMC3091709 DOI: 10.1186/1471-2164-11-560] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Accepted: 10/12/2010] [Indexed: 01/30/2023] Open
Abstract
Background Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes. Results The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase. Conclusions This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.
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Affiliation(s)
- Jean-Francois Martin
- Centre de biologie et de gestion des Populations, Montpellier SupAgro, INRA, IRD, CIRAD, Campus International de Baillarguet, CS30016, Montferrier sur Lez cedex, France.
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Genome-based microsatellite development in the Culex pipiens complex and comparative microsatellite frequency with Aedes aegypti and Anopheles gambiae. PLoS One 2010; 5. [PMID: 20927334 PMCID: PMC2948009 DOI: 10.1371/journal.pone.0013062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/04/2010] [Indexed: 11/29/2022] Open
Abstract
Background Mosquitoes in the Culex pipiens complex are among the most medically important vectors for human disease worldwide and include major vectors for lymphatic filariasis and West Nile virus transmission. However, detailed genetic studies in the complex are limited by the number of genetic markers available. Here, we describe methods for the rapid and efficient identification and development of single locus, highly polymorphic microsatellite markers for Cx. pipiens complex mosquitoes via in silico screening of the Cx. quinquefasciatus genome sequence. Methodology/Principal Findings Six lab colonies representing four Cx. pipiens and two Cx. quinquefasciatus populations were utilized for preliminary assessment of 38 putative loci identified within 16 Cx. quinquefasciatus supercontig assemblies (CpipJ1) containing previously mapped genetic marker sequences. We identified and validated 12 new microsatellite markers distributed across all three linkage groups that amplify consistently among strains representing the complex. We also developed four groups of 3–5 microsatellite loci each for multiplex-ready PCR. Field collections from three cities in Indiana were used to assess the multiplex groups for their application to natural populations. All were highly polymorphic (Mean = 13.0 alleles) per locus and reflected high polymorphism information content (PIC) (Mean = 0.701). Pairwise FST indicated population structuring between Terre Haute and Fort Wayne and between Terre Haute and Indianapolis, but not between Fort Wayne and Indianapolis. In addition, we performed whole genome comparisons of microsatellite motifs and abundance between Cx. quinquefasciatus and the primary vectors for dengue virus and malaria parasites, Aedes aegypti and Anopheles gambiae, respectively. Conclusions/Significance We demonstrate a systematic approach for isolation and validation of microsatellites for the Cx. pipiens complex by direct screen of the Cx. quinquefasciatus genome supercontig assemblies. The genome density of microsatellites is greater in Cx. quinquefasciatus (0.26%) than in Ae. aegypti (0.14%), but considerably lower than in An. gambiae (0.77%).
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Tay WT, Behere GT, Batterham P, Heckel DG. Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes. BMC Evol Biol 2010; 10:144. [PMID: 20470440 PMCID: PMC2887409 DOI: 10.1186/1471-2148-10-144] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2009] [Accepted: 05/17/2010] [Indexed: 11/10/2022] Open
Abstract
Background Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. These families are thought to be associated with unequal crossing-over during DNA recombination or with transposable elements (TEs). Results We identified full-length lepidopteran non-LTR retrotransposable elements of the RTE clade in Heliconius melpomene and Bombyx mori. These retroelements possess a single open reading frame encoding the Exonuclease/Endonuclease/Phosphatase and the Reverse Transcriptase/nLTR domains, a 5' UTR (untranslated region), and an extremely short 3' UTR that regularly consists of SSR units. Phylogenetic analysis supported previous suggestions of horizontal transfer among unrelated groups of organisms, but the diversity of lepidopteran RTE elements appears due to ancient divergence of ancestral elements rather than introgression by horizontal transfer. Similarity searches of lepidopteran genomic sequences in GenBank identified partial RTE elements, usually consisting of the 3' terminal region, in 29 species. Furthermore, we identified the C-terminal end of the Reverse Transcriptase/nLTR domain and the associated 3' UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in GenBank. Occasional retrotransposition of autonomous elements, frequent retrotransposition of 3' partial elements, and DNA replication slippage during retrotransposition offers a mechanistic explanation for the association of SSRs with RTE elements in lepidopteran genomes. Conclusions Non-LTR retrotransposable elements of the RTE clade therefore join a diverse group of TEs as progenitors of SSR units in various organisms. When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated regions, amplification from multiple genomic sites can cause scoring difficulties that compromise their utility as markers. Screening against RTE elements in the isolation procedure provides one strategy for minimizing this problem.
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Affiliation(s)
- Wee Tek Tay
- Centre for Environmental Stress and Adaptation Research, Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville 3010, Australia
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Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs. Heredity (Edinb) 2010; 106:78-87. [PMID: 20424639 DOI: 10.1038/hdy.2010.36] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.
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Coates BS, Sumerford DV, Hellmich RL, Lewis LC. A helitron-like transposon superfamily from lepidoptera disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family. J Mol Evol 2010; 70:275-88. [PMID: 20217059 DOI: 10.1007/s00239-010-9330-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/17/2010] [Indexed: 12/20/2022]
Abstract
Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)(n) microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)(n) microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)(n) microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)(n) microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.
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Pannebakker BA, Niehuis O, Hedley A, Gadau J, Shuker DM. The distribution of microsatellites in the Nasonia parasitoid wasp genome. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 1:91-8. [PMID: 20167020 DOI: 10.1111/j.1365-2583.2009.00915.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microsatellites are important molecular markers used in numerous genetic contexts. Despite this widespread use, the evolutionary processes governing microsatellite distribution and diversity remain controversial. Here, we present results on the distribution of microsatellites of three species in the parasitic wasp genus Nasonia generated by an in silico data-mining approach. Our results show that the overall microsatellite density in Nasonia is comparable to that of the honey bee, but much higher than in eight non-Hymenopteran arthropods. Across the Nasonia vitripennis genome, microsatellite density varied both within and amongst chromosomes. In contrast to other taxa, dinucleotides are the most abundant repeat type in all four species of Hymenoptera studied. Whether the differences between the Hymenoptera and other taxa are of functional significance remains to be determined.
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Affiliation(s)
- B A Pannebakker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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Luchetti A, Mantovani B. Talua SINE Biology in the Genome of the Reticulitermes Subterranean Termites (Isoptera, Rhinotermitidae). J Mol Evol 2009; 69:589-600. [DOI: 10.1007/s00239-009-9285-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
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Isolation and characterization of eight microsatellite loci in the spruce budworm species Choristoneura fumiferana and Choristoneura occidentalis, and cross-species amplification in related tortricid moths. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9116-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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