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Varshney S, Sagwekar M, Pavan-Kumar A, Das R, Gireesh-Babu P, Chaudhari A, Krishna G. Development and characterisation of novel polymorphic microsatellite loci in the freshwater mussel Lamellidens marginalis (Lamarck, 1819) using next generation sequencing. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1799147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Shubham Varshney
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Madhavi Sagwekar
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - A. Pavan-Kumar
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Rekha Das
- Division of Fisheries, ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, India
| | - P. Gireesh-Babu
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Aparna Chaudhari
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Gopal Krishna
- Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Fisheries Education, Mumbai, India
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2
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Ciminera M, Auger-Rozenberg MA, Caron H, Herrera M, Scotti-Saintagne C, Scotti I, Tysklind N, Roques A. Genetic Variation and Differentiation of Hylesia metabus (Lepidoptera: Saturniidae): Moths of Public Health Importance in French Guiana and in Venezuela. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:137-148. [PMID: 30272198 DOI: 10.1093/jme/tjy167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Hylesia moths impact human health in South America, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of females' abdominal setae. The classification of the Hylesia genus is complex, owing to its high diversity in Amazonia, high intraspecific morphological variance, and lack of interspecific diagnostic traits which may hide cryptic species. Outbreaks of Hylesia metabus have been considered responsible for the intense outbreaks of lepidopterism in Venezuela and French Guiana since the C20, however, little is known about genetic variability throughout the species range, which is instrumental for establishing control strategies on H. metabus. Seven microsatellites and mitochondrial gene markers were analyzed from Hylesia moths collected from two major lepidopterism outbreak South American regions. The mitochondrial gene sequences contained significant genetic variation, revealing a single, widespread, polymorphic species with distinct clusters, possibly corresponding to populations evolving in isolation. The microsatellite markers validated the mitochondrial results, and suggest the presence of three populations: one in Venezuela, and two in French Guiana. All moths sampled during outbreak events in French Guiana were assigned to a single coastal population. The causes and implications of this finding require further research.
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Affiliation(s)
- Marina Ciminera
- CNRS, UMR0745 Ecologie des Forêts de Guyane (EcoFoG), AgroParisTech, Cirad, INRA, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, Kourou Cedex, France
| | | | - Henri Caron
- INRA, UMR0745 Ecologie des Forêts de Guyane (EcoFoG), AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, Kourou Cedex, France
| | - Melfran Herrera
- Coordinación de Vigilancia Entomológica, Gerencia de Saneamiento Ambiental y Control de Endemias, FUNDASALUD, Carúpano, Estado Sucre, Venezuela
| | | | - Ivan Scotti
- INRA, UR629, Unité de Recherche Ecologie des forêts méditerranéennes, Avignon, France
| | - Niklas Tysklind
- INRA, UMR0745 Ecologie des Forêts de Guyane (EcoFoG), AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, Kourou Cedex, France
| | - Alain Roques
- INRA, UR633, Zoologie Forestière, Orléans, France
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3
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Saarman NP, Kober KM, Simison WB, Pogson GH. Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis). Genome Biol Evol 2018; 9:2739-2751. [PMID: 28985307 PMCID: PMC5647807 DOI: 10.1093/gbe/evx190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 12/12/2022] Open
Abstract
Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage. Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis’ superior tolerance to heat stress, and that pairing tests for positive selection and tests for transcriptional response to heat stress can identify candidates of protein stability adaptation.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Ecology and Evolutionary Biology, Yale University
| | - Kord M Kober
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Physiological Nursing, University of California, San Francisco.,Institute for Computational Health Sciences, University of California, San Francisco
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
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4
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Khimoun A, Ollivier A, Faivre B, Garnier S. Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs. Mol Ecol Resour 2017; 17:893-903. [PMID: 27978606 DOI: 10.1111/1755-0998.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/26/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022]
Abstract
Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
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Affiliation(s)
- Aurélie Khimoun
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
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5
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Saarman NP, Pogson GH. Introgression between invasive and native blue mussels (genusMytilus) in the central California hybrid zone. Mol Ecol 2015; 24:4723-38. [DOI: 10.1111/mec.13340] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Norah P. Saarman
- Department of Ecology and Evolutionary Biology; Yale University; PO Box 208106 New Haven CT 06520-8106 USA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary Biology; UC Santa Cruz; Santa Cruz CA 95064 USA
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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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7
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Zhao C, Zhang T, Zhang X, Hu S, Xiang J. Sequencing and analysis of four BAC clones containing innate immune genes from the Zhikong scallop (Chlamys farreri). Gene 2012; 502:9-15. [PMID: 22542508 DOI: 10.1016/j.gene.2012.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/29/2012] [Accepted: 04/05/2012] [Indexed: 11/17/2022]
Abstract
The sequencing of BAC clones (~100 kb) can reveal some characteristics of a genome that are challenging to obtain based on short sequences. Additionally, although the immune genes of the Zhikong scallop (Chlamys farreri) have been studied widely, few analyses have been conducted at the DNA level. In this study, four C. farreri BAC clones containing innate immune genes, including hsp70, l gbp (lipopolysaccharide and beta-1,3-glucan binding protein), serine protease and a gene with an immunoglobulin-like domain, were sequenced and analyzed both to explore the genomic characteristics of C. farreri based on long DNA sequences and to promote the study of C. farreri immune genes at the DNA level. The total length of the four BACs was 389.98 kb. A total of 34 genes were predicted in these sequences, and several features of protein-coding regions in the C. farreri genome were inferred based on this information. Two LGBP genes were located close together in a 22-kb region in one BAC clone, indicating the physical linkage of some immune genes in C. farreri. A cluster of membrane transport genes was also observed; these genes might play important roles in eliminating toxins in C. farreri, which lives as a filter feeder. Further analysis showed 15.43% of the BAC sequence was repetitive. Tandem repeats were the most abundant repeat type, followed by transposable elements. A total of 31 SSRs were predicted in the four BACs. An IS10 family transposon was identified, and a suspected regulatory non-coding RNA gene for this transposon (RNA-OUT) was observed to overlap with it complementarily. This work will promote future studies on the genomics, immune system and non-coding regions of C. farreri.
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Affiliation(s)
- Cui Zhao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
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Wild and hatchery populations of Korean starry flounder (Platichthys stellatus) compared using microsatellite DNA markers. Int J Mol Sci 2012; 12:9189-202. [PMID: 22272127 PMCID: PMC3257124 DOI: 10.3390/ijms12129189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022] Open
Abstract
Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity.
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Wang H, Huan P, Lu X, Liu B. Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome. Genes Genet Syst 2012; 86:197-205. [PMID: 21952209 DOI: 10.1266/ggs.86.197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A total of 2,970 EST-SSRs (2.38%) were identified by transcriptome sequencing of clam Meretrix meretrix (751,970 reads, ~310.82 Mbp), using 454 Genome Sequencer FLX next-generation sequencing platform. Dinucleotide SSR was the dominant repeat type (40.2%), followed by trinucleotide (37.8%), tetranuleotide (12.0%) and pentanucleotide (2.0%) SSR. The dominant repeat motif was AT (71.3%) in the dinucleotide SSR type and AAC (45.6%) in the trinucleotide SSR type. Nearly 79% of all microsatellites had flanking sequences suitable for PCR primer design. Half of PAL were found to be polymorphic in a subset of 40 primer pairs randomly selected. Specifically, the density of dinucleotide, trinucleotide and tetranucleotide repeats showed significant variation among four development stages (trochophore, D-veliger, pediveliger and postlarva). The results suggested that dinucleotide, trinucleotide and tetranucleotide SSRs may play an important role in contributing to the different expression profiles in larval stages.
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Affiliation(s)
- Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Quingdao, China
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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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An HS, Kim BH, Lee JW, Dong CM, Kim SK, Kim YC. Comparison between wild and hatchery populations of Korean pen shell (Atrina pectinata) using microsatellite DNA markers. Int J Mol Sci 2011; 12:6024-39. [PMID: 22016642 PMCID: PMC3189766 DOI: 10.3390/ijms12096024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 12/02/2022] Open
Abstract
Pen shell (Atrina pectinata) is a popular food source with a high commercial value in a number of Asian Pacific areas. The natural A. pectinata population has been declining continuously over the past several decades. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of pen shell populations. In this study, 20 polymorphic microsatellite (MS) DNA markers were identified from a partial genomic pen shell DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery pen shell populations in Korea. A total of 438 alleles were detected at the 20 MS loci in the two populations. All loci were easily amplified and demonstrated allelic variability, with the number of alleles ranging from 5 to 35 in the wild population and from 5 to 22 in the farmed population. The average observed and expected heterozygosities were 0.69 and 0.82, respectively, in the hatchery samples and 0.69 and 0.83, respectively, in the wild samples. Statistical analysis of fixation index (FST) and analysis of molecular variance (AMOVA) showed minor, but significant, genetic differences between the wild and hatchery populations (FST = 0.0106, CI95% = 0.003–0.017). These microsatellite loci may be valuable for future aquaculture and population genetic studies for developing conservation and management plans. Further studies with additional pen shell samples are needed to conclusively determine the genetic diversity between the wild and hatchery populations.
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Affiliation(s)
- Hye Suck An
- New Strategy Research Center, National Fisheries Research and Development Institute, Busan 619-705, Korea; E-Mails: (B.H.K.); (J.W.L.); (C.M.D.); (S.K.K.); (Y.C.K.)
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12
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Jun TH, Michel AP, Mian MAR. Development of soybean aphid genomic SSR markers using next generation sequencing. Genome 2011; 54:360-7. [PMID: 21529140 DOI: 10.1139/g11-002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid (Aphis glycines Matsumura) has become the most damaging insect pest of soybean (Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.
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Affiliation(s)
- Tae-Hwan Jun
- Department of Entomology, The Ohio State University - Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
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Ellison CK, Shaw KL. Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness. BMC Genomics 2010; 11:428. [PMID: 20624300 PMCID: PMC2996956 DOI: 10.1186/1471-2164-11-428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 07/12/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC) libraries and expressed sequence tag (EST) libraries. RESULTS 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. CONCLUSION The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications.
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Affiliation(s)
| | - Kerry L Shaw
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
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Mikheyev AS, Vo T, Wee B, Singer MC, Parmesan C. Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances. PLoS One 2010; 5:e11212. [PMID: 20585453 PMCID: PMC2887849 DOI: 10.1371/journal.pone.0011212] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 04/26/2010] [Indexed: 12/03/2022] Open
Abstract
Background The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). Principal Findings By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations). Significance De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.
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VIDAL R, PEÑALOZA C, URZÚA R, TORO JE. Screening of ESTs from
Mytilus
for the detection of SSR markers in
Mytilus californianus. Mol Ecol Resour 2009; 9:1409-11. [DOI: 10.1111/j.1755-0998.2009.02682.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. VIDAL
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Avda. Libertador Bernardo O′Higgins 3363, Santiago, Chile
| | - C. PEÑALOZA
- Instituto de Biología Marina, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - R. URZÚA
- Center for Bioinformatics and Molecular Simulations, University of Talca, Chile. 2 Norte 685, Talca, Chile
| | - J. E. TORO
- Instituto de Biología Marina, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
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Xu Z, Gutierrez L, Hitchens M, Scherer S, Sater AK, Wells DE. Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis. Bioinform Biol Insights 2008; 2:157-69. [PMID: 19812773 PMCID: PMC2735965 DOI: 10.4137/bbi.s561] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
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Affiliation(s)
- Zhenkang Xu
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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18
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Kim KS, Ratcliffe ST, French BW, Liu L, Sappington TW. Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle. J Hered 2008; 99:112-24. [DOI: 10.1093/jhered/esm104] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Tanguy A, Bierne N, Saavedra C, Pina B, Bachère E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapègue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, Canario A. Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution. Gene 2008; 408:27-36. [DOI: 10.1016/j.gene.2007.10.021] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Revised: 10/05/2007] [Accepted: 10/13/2007] [Indexed: 10/22/2022]
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20
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YU HONG, LI QI. Development of EST-SSRs in the Mediterranean blue mussel, Mytilus galloproviancialis. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01865.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Zhang L, Chen C, Cheng J, Wang S, Hu X, Hu J, Bao Z. Initial analysis of tandemly repetitive sequences in the genome of Zhikong scallop (Chlamys farreri Jones et Preston). DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2007; 19:195-205. [PMID: 17852361 DOI: 10.1080/10425170701462316] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Tandemly repetitive sequences are widespread in all eukaryotic genomes, but data on tandem repeats are limited in Zhikong scallop (Chlamys farreri). In the present study, paired-end sequencing of 2016 individual fosmid clones resulted in 3646 sequences. A total of 2,286,986 bp of genomic sequences were generated, representing approximately 1.84 per thousand of the Zhikong scallop genome. Using tandem repeats finder (TRF) software, a total of 2500 tandem repeats were found, including 313 satellites, 1816 minisatellites and 371 microsatellites. The cumulative length of tandem repeats was 552,558 bp, accounting for 24.16% of total length. Specifically, the length of microsatellites, minisatellites and satellites was 9425, 336,001 and 207,132 bp, accounting for 1.71, 60.81 and 37.49% of the length of tandem repeats, and 0.41, 14.69 and 9.06% of total length, respectively. The detailed information on the characteristic of all repeat units was also represented, which will provide a useful resource for physical mapping and better utilization of the existing genomic information in Zhikong scallop.
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Affiliation(s)
- Lingling Zhang
- Division of Life Science and Technology, Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, People's Republic of China.
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22
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Biscotti MA, Canapa A, Olmo E, Barucca M, Teo CH, Schwarzacher T, Dennerlein S, Richter R, Heslop-Harrison JSP. Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus). Gene 2007; 406:91-8. [PMID: 17706376 DOI: 10.1016/j.gene.2007.06.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 06/15/2007] [Accepted: 06/25/2007] [Indexed: 11/26/2022]
Abstract
We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.
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Abdelkrim J, Pascal M, Samadi S. Establishing causes of eradication failure based on genetics: case study of ship rat eradication in Ste. Anne archipelago. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2007; 21:719-30. [PMID: 17531050 DOI: 10.1111/j.1523-1739.2007.00696.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Determining the causes of a failed eradication of a pest species is important because it enables an argued adjustment of the methodologies used and the improvement of the protocols for future attempts. We examined how molecular monitoring can help distinguish between the two main reasons for an eradication failure (i.e., survival of some individuals vs. recolonization after eradication). We investigated genetic variation in seven microsatellite loci in ship rat (Rattus rattus) populations from four islets off the Martinique coast (French Caribbean). In 1999 an eradication attempt was conducted on the four islets. Three years later rats were observed again on two of them. We compared the genetic signatures of the populations before and after the eradication attempt. On one of the islands, the new rat population was likely a subset of the pre-eradication population. A weak genetic differentiation was found between them, with almost no new alleles observed in the new population and moderate F(ST) values (0.15). Moreover, assignment procedures clustered the two populations together. In contrast, on the other islet, many new alleles were observed after the eradication attempt, resulting in an increase in genetic diversity (from 2.57 to 3.57 mean number of alleles per locus) and strong F(ST) values (0.39). Moreover, genetic clustering clearly separated the two samples (i.e., before and after the eradication attempt) in two different populations. Thus, to achieve long-term eradication on these islets, it seems necessary to redevelop the eradication procedure to avoid individuals surviving and to prevent reinvasion, probably from the mainland, by installing permanent trapping and poisoning devices and conducting regular monitoring. We strongly encourage wildlife managers conducting eradication campaigns to integrate molecular biological tools in their protocols, which can be done easily for most common invasive species.
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Affiliation(s)
- Jawad Abdelkrim
- UMR 7138: CNRS, IRD, Muséum National d'Histoire Naturelle, Université de Paris 6, Systématique, Adaptation, Evolution, Département de Systématique et Evolution, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75003 Paris, France.
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24
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Malysheva DN, Tokarskaya ON, Petrosyan VG, Danielyan FD, Darevsky IS, Ryskov AP. Genomic variation in parthenogenetic lizard Darevskia armeniaca: evidence from DNA fingerprinting data. ACTA ACUST UNITED AC 2007; 98:173-8. [PMID: 17374876 DOI: 10.1093/jhered/esm003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Microsatellites, or short tandem repeats, are abundant across genomes of most organisms. It is evident that the most straightforward and conclusive way of studying mutations in microsatellite-containing loci is to use clonally transmitted genomes or DNA sequences inherited in multigeneration pedigrees. At present, little is known about the origin of genetic variation in species that lack effective genetic recombination. DNA fingerprinting in 43 families of the parthenogenetic lizard species Darevskia armeniaca (131 siblings), using (GACA)(4), (GGCA)(4), (GATA)(4), and (CAC)(5) probes, revealed mutant fingerprints in siblings that differed from their mothers in several restriction DNA fragments. In some cases, the mutant fingerprints detected in siblings were also found in population samples. The mutation rate for new restriction fragment length estimated by using multilocus probes varied from 0.8 x 10(-2) to 4.9 x 10(-2) per band/per sibling. Probably, the most variations detected as restriction fragment length polymorphism have germ-line origin, but somatic changes of (CAC)(n) fingerprints in adult lizards were also observed. These results provide new evidence of existing unstable regions in genomes of parthenogenetic vertebrate animals, which provide genetic variation in unisexual populations.
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Affiliation(s)
- D N Malysheva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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Buschiazzo E, Gemmell NJ. The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays 2006; 28:1040-50. [PMID: 16998838 DOI: 10.1002/bies.20470] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.
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Affiliation(s)
- Emmanuel Buschiazzo
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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26
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Selkoe KA, Toonen RJ. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 2006; 9:615-29. [PMID: 16643306 DOI: 10.1111/j.1461-0248.2006.00889.x] [Citation(s) in RCA: 747] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists' ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike.
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Affiliation(s)
- Kimberly A Selkoe
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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Rabello E, Souza AND, Saito D, Tsai SM. In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations. Genet Mol Biol 2005. [DOI: 10.1590/s1415-47572005000400013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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