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Koubínová D, GoFlag Consortium, Grant JR. Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae. PLANTS (BASEL, SWITZERLAND) 2024; 13:713. [PMID: 38475562 DOI: 10.3390/plants13050713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 03/14/2024]
Abstract
Microsatellites or SSRs are small tandem repeats that are 1-6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases.
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Affiliation(s)
- Darina Koubínová
- Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland
| | - GoFlag Consortium
- Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland
| | - Jason R Grant
- Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland
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Choquet M, Lizano AM, Le Moan A, Ravinet M, Dhanasiri AKS, Hoarau G. Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus. Mol Ecol 2023; 32:6854-6873. [PMID: 37902127 DOI: 10.1111/mec.17183] [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: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.
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Affiliation(s)
- Marvin Choquet
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Alan Le Moan
- CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Anusha K S Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Sawai K, Arakawa A, Taniguchi M, Xiao B, Sawai M, Osaki M, Yamaguchi E, Hayama Y, Murato Y, Shimizu Y, Kondo S, Yamamoto T. Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan. Sci Rep 2023; 13:21186. [PMID: 38040788 PMCID: PMC10692317 DOI: 10.1038/s41598-023-48215-0] [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: 06/26/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023] Open
Abstract
Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.
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Affiliation(s)
- Kotaro Sawai
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Aisaku Arakawa
- Meat Animal Biosystems Group, Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
| | - Masaaki Taniguchi
- Meat Animal Biosystems Group, Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
| | - Bo Xiao
- Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Miwa Sawai
- Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Makoto Osaki
- Division of Hygiene Management Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Emi Yamaguchi
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yoko Hayama
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yoshinori Murato
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yumiko Shimizu
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Sonoko Kondo
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Takehisa Yamamoto
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan.
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4
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Bruno Agudo A, Xavier Picó F, Mateo RG, Marcer A, Torices R, Álvarez I. Unravelling plant diversification: Intraspecific genetic differentiation in hybridizing Anacyclus species in the western Mediterranean Basin. AMERICAN JOURNAL OF BOTANY 2023; 110:e16121. [PMID: 36541247 DOI: 10.1002/ajb2.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
PREMISE The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters. METHODS We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters. RESULTS We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas. CONCLUSIONS Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.
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Affiliation(s)
- A Bruno Agudo
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología y Evolución, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Rubén G Mateo
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Arnald Marcer
- CREAF, E 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Universitat Autònoma de Barcelona, E 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Rubén Torices
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Inés Álvarez
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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5
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Wolf KKE, Hoppe CJM, Leese F, Weiss M, Rost B, Neuhaus S, Gross T, Kühne N, John U. Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach. Environ Microbiol 2021; 23:3809-3824. [PMID: 33559305 DOI: 10.1111/1462-2920.15424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/28/2022]
Abstract
Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.
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Affiliation(s)
- Klara K E Wolf
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Clara J M Hoppe
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Björn Rost
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Bremen, FB2, Bremen, Germany
| | - Stefan Neuhaus
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Thilo Gross
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Oldenburg, ICBM, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Nancy Kühne
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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6
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Viruel J, Haguenauer A, Juin M, Mirleau F, Bouteiller D, Boudagher‐Kharrat M, Ouahmane L, La Malfa S, Médail F, Sanguin H, Nieto Feliner G, Baumel A. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). APPLICATIONS IN PLANT SCIENCES 2018; 6:e01201. [PMID: 30598859 PMCID: PMC6303155 DOI: 10.1002/aps3.1201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/28/2018] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. METHODS In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. RESULTS The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
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Affiliation(s)
- Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Anne Haguenauer
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Marianick Juin
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Fatma Mirleau
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM)Hôpital Pitié Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
| | - Magda Boudagher‐Kharrat
- Laboratoire Caractérisation Génétique des PlantesFaculté des sciencesUniversité Saint‐JosephB.P. 11‐514 Riad El SolhBeirut1107 2050Lebanon
| | - Lahcen Ouahmane
- Laboratoire d'Ecologie et EnvironnementFaculté des Sciences SemlaliaUniversité Cadi AyyadMarrakeshMorocco
| | - Stefano La Malfa
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A)Università degli Studi di CataniaVia Valdisavoia 595123CataniaItaly
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Hervé Sanguin
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD)Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM)MontpellierFrance
- LSTM [LSTM is sponsored by University of Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro]TA A‐82/J Campus International de BaillarguetFR‐34398Montpellier CEDEX 5France
| | | | - Alex Baumel
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
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Šarhanová P, Pfanzelt S, Brandt R, Himmelbach A, Blattner FR. SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring. Ecol Evol 2018; 8:10817-10833. [PMID: 30519409 PMCID: PMC6262739 DOI: 10.1002/ece3.4533] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 01/13/2023] Open
Abstract
Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next-generation sequencing (NGS) makes it easy to obtain also sequence information for the loci of interest. This avoids misinterpretations that otherwise could arise due to size homoplasy. Here, an NGS strategy is described that allows to genotype hundreds of individuals at many custom-designed SSR loci simultaneously, combining multiplex PCR, barcoding, and Illumina sequencing. We created three different datasets for which alleles were coded according to (a) length of the repetitive region, (b) total fragment length, and (c) sequence identity, in order to evaluate the eventual benefits from having sequence data at hand, not only fragment length data. For each dataset, genetic diversity statistics, as well as F ST and R ST values, were calculated. The number of alleles per locus, as well as observed and expected heterozygosity, was highest in the sequence identity dataset, because of single-nucleotide polymorphisms and insertions/deletions in the flanking regions of the SSR motif. Size homoplasy was found to be very common, amounting to 44.7%-63.5% (mean over all loci) in the three study species. Thus, the information obtained by next-generation sequencing offers a better resolution than the traditional way of SSR genotyping and allows for more accurate evolutionary interpretations.
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Affiliation(s)
- Petra Šarhanová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address:
Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Simon Pfanzelt
- Institute of Biology and Environmental SciencesCarl von Ossietzky University OldenburgOldenburgGermany
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Ronny Brandt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address:
Max Planck Genome Centre CologneCologneGermany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Frank R. Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
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8
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Swift JF, Lance RF, Guan X, Britzke ER, Lindsay DL, Edwards CE. Multifaceted DNA metabarcoding: Validation of a noninvasive, next-generation approach to studying bat populations. Evol Appl 2018; 11:1120-1138. [PMID: 30026801 PMCID: PMC6050187 DOI: 10.1111/eva.12644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
As multiple species of bats are currently experiencing dramatic declines in populations due to white-nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once-common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high-throughput, DNA-based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next-generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics.
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Affiliation(s)
- Joel F. Swift
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSt. LouisMissouri
| | - Richard F. Lance
- Environmental LaboratoryUS Army Engineer Research and Development CenterVicksburgMississippi
| | - Xin Guan
- Bennett AerospaceCaryNorth Carolina
| | - Eric R. Britzke
- Environmental LaboratoryUS Army Engineer Research and Development CenterVicksburgMississippi
| | - Denise L. Lindsay
- Environmental LaboratoryUS Army Engineer Research and Development CenterVicksburgMississippi
| | - Christine E. Edwards
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSt. LouisMissouri
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9
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Šarhanová P, Sharbel TF, Sochor M, Vašut RJ, Dančák M, Trávníček B. Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers. ANNALS OF BOTANY 2017; 120:317-328. [PMID: 28402390 PMCID: PMC5737493 DOI: 10.1093/aob/mcx033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/02/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Rubus subgenus Rubus is a group of mostly apomictic and polyploid species with a complicated taxonomy and history of ongoing hybridization. The only polyploid series with prevailing sexuality is the series Glandulosi , although the apomictic series Discolores and Radula also retain a high degree of sexuality, which is influenced by environmental conditions and/or pollen donors. The aim of this study is to detect sources of genetic variability, determine the origin of apomictic taxa and validate microsatellite markers by cloning and sequencing. METHODS A total of 206 individuals from two central European regions were genotyped for 11 nuclear microsatellite loci and the chloroplast trn L- trn F region. Microsatellite alleles were further sequenced in order to determine the exact repeat number and to detect size homoplasy due to insertions/deletions in flanking regions. KEY RESULTS The results confirm that apomictic microspecies of ser. Radula are derived from crosses between sexual series Glandulosi and apomictic series Discolores , whereby the apomict acts as pollen donor. Each apomictic microspecies is derived from a single distinct genotype differing from the parental taxa, suggesting stabilized clonal reproduction. Intraspecific variation within apomicts is considerably low compared with sexual series Glandulosi , and reflects somatic mutation accumulation. While facultative apomicts produce clonal offspring, sexual species are the conduits of origin for new genetically different apomictic lineages. CONCLUSIONS One of the main driving forces of evolution and speciation in the highly apomictic subgenus Rubus in central Europe is sexuality in the series Glandulosi . Palaeovegetation data suggest that initial hybridizations took place over different time periods in the two studied regions, and that the successful origin and spread of apomictic microspecies of the series Radula took place over several millennia. Additionally, the cloning and sequencing show that standard evaluations of microsatellite repeat numbers underestimate genetic variability considering homoplasy in allele size.
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Affiliation(s)
- Petra Šarhanová
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Department of Experimental Taxonomy, Corrensstr. 3, D-06466 Gatersleben, Germany
- For correspondence. E-mail
| | - Timothy F. Sharbel
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Department of Experimental Taxonomy, Corrensstr. 3, D-06466 Gatersleben, Germany
- Present address: Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place, suite 1460 Saskatoon, SK S7N 4J8, Canada
| | - Michal Sochor
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, CZ-78371 Olomouc, Czech Republic
| | - Radim J. Vašut
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Martin Dančák
- Department of Ecology and Environmental Sciences, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Bohumil Trávníček
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
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No rest for the laurels: symbiotic invaders cause unprecedented damage to southern USA forests. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1427-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mayland-Quellhorst E, Meudt HM, Albach DC. Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600091. [PMID: 27785388 PMCID: PMC5077287 DOI: 10.3732/apps.1600091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY Polyploidy may generate novel variation, leading to adaptation and species diversification. An excellent natural system to study polyploid evolution in a comparative framework is Veronica (Plantaginaceae), which comprises several parallel, recently evolved polyploid series. METHODS Over 105 million Illumina paired-end sequence reads were generated from cDNA libraries of leaf tissue from eight individuals representing three European and four New Zealand species. Forty-eight simple sequence repeat (SSR) and 48 low-copy nuclear (LCN) markers were developed and validated with Fluidigm microfluidic PCR and Illumina MiSeq amplicon sequencing on 48 different individuals each. RESULTS Individual Trinity assemblies were similar regarding annotated transcripts (13,009-14,271), mean contig length (635-742 bp), N50 value (916-1133 bp), E90N50 value (1099-1308 bp), contigs with positive BLAST hits (42-63%), and gene ontology terms. Analyses of 29,738 single-nucleotide polymorphisms (8746 phylogenetically informative) mined from these transcriptomes plus two outgroups (Picrorhiza kurrooa and Plantago ovata) showed moderate to high bootstrap support for all branches and reticulation among sampled European Veronica. DISCUSSION The transcriptome sequences themselves, as well as the validated SSR (40/48) and LCN (11/48) markers derived from them, show inter- and intraspecific genetic variation. These resources will be invaluable for future population genetic, phylogenetic, and functional genetic investigations in polyploid Veronica.
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Affiliation(s)
- Eike Mayland-Quellhorst
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
| | - Heidi M. Meudt
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
- Museum of New Zealand Te Papa Tongarewa, Cable Street, P.O. Box 467, Wellington 6140, New Zealand
| | - Dirk C. Albach
- Carl-von-Ossietzky Universität Oldenburg, Carl-von-Ossietzky Straße 9–11, Oldenburg 26111, Germany
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