Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle (original) (raw)
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Nucleotide sequence information available in searchable sequence databases and the free in silico software with which to extract and analyze microsatellite data continues to grow at a rapid rate across eukaryote taxa. The sheer amount of information available means that a comprehensive or exhaustive review of databases and free bioinformatic tools lies beyond the purview of any journal review. The purpose of this review is therefore to provide targeted information aimed at helping the insect and plant biologist effectively utilize in silico resources to find, navigate and analyze empirically derived data from sequence databases. The objectives are threefold. First, since the basic characteristics of microsatellites make them the markers of choice for studies of genetic structure that underlie adaptation and evolution, these will be delineated. Second, because sequence databases are increasingly mined for microsatellites, the major databases are discussed, as well as, available programs for in silico mining of sequence databases to retrieve microsatellites for a species of interest. Lastly, a general review is given of population genetics software for in silico genetic analyses of microsatellite data to determine population genetic structure, phylogenetic relationships, and genetic diversity in a species of interest.
Microsatellite DNA markers for two endemic ground beetles: Carabus punctatoauratus and C. solieri
Molecular Ecology Notes, 2002
We isolated and characterized nine and five polymorphic microsatellite loci in the respective ground beetles Carabus punctatoauratus and C. solieri. We tested cross-species amplification of all these loci plus six isolated in C. solieri and for which primers sequences were soon published. From these combined analyses, we obtained 14 and 17 polymorphic markers, respectively, for C. punctatoauratus and C. solieri .
Microsatellite DNA markers for the ground beetle Pterostichus oblongopunctatus F
Molecular Ecology Notes, 2004
Six microsatellite DNA loci were isolated from the ground beetle Pterostichus oblongopunctatus F. (Coleoptera, Carabidae) to study population structure. Each locus was polymorphic, with the number of alleles ranging from three to six. Observed heterozygosity varied between 0.20 and 0.67. All six loci were tested for amplification in the closely related P. quadrifoveolatus and they were shown to be polymorphic. The primers developed were used in multiplex polymerase chain reactions.
Journal of molecular evolution, 2007
Microsatellites are powerful markers often isolated de novo for species yet to be investigated. Enriched genomic libraries are usually used for isolation purposes. We critically evaluate the outcome of an enrichment-based protocol applied to two insect species (the ant Lasius austriacus and the beetle Pityogenes chalcographus) which yielded contrasting numbers of suitable loci. Our findings of differences in microsatellite isolation are consistent with the available data on differences in genomic characteristics across these taxa. In the beetle repeated isolation of identical motifs, difficulties in primer development, and multibanded products caused loss of most candidate clones. We identified critical steps during marker development.
European Journal of Entomology
The European stag beetle, Lucanus cervus, is recognised as a fl agship species for biodiversity conservation. Although the species is widely distributed across Europe declines have led to it being granted protected or endangered status in a number of countries and regarded as "near threatened" by the IUCN. The integration of genetic approaches into conservation efforts is urgently needed but has been impeded to date by the lack of appropriate genetic markers. To provide such a resource the development of the fi rst microsatellite loci for stag beetle is described. Loci were identifi ed using two methods (i) enriched library cloning (ELC) and (ii) Restriction enzyme Associated DNA sequencing (RAD-Seq). Ineffi cient microsatellite detection using the ELC method suggests that RAD-Seq, or other Next Generation Sequencing based methods, may ultimately be more cost effective for obtaining informative suites of markers for this and other coleopteran species. 18 loci were characterised by genotyping 42 UK specimens collected as prey leftover/roadkill. All loci produced unambiguous genotypes and were polymorphic. Though preliminary, estimates of genetic variability suggest UK populations may be genetically depauperate. The microsatellite loci represent a suite of genetic markers that can be applied to non-invasive population monitoring and numerous other areas of Lucanus conservation and evolutionary research.
Identification of microsatellite markers in the red flour beetle, Tribolium castaneum
Molecular Ecology Notes, 2003
We isolated and characterized microsatellite markers for the red flour beetle Tribolium castaneum , an important model species for studies in various areas of evolutionary biology and ecology. A microsatellite-enriched genomic library was constructed and screened with single stranded oligonucleotide probes [(CCT) 17 , (AAT) 17 and (CAG) 17 ]. Forty-five primer pairs were designed of which 19 pairs produced successful amplification. Polymorphism screening involved beetles from five beetle strains and revealed 15 polymorphic and four monomorphic markers. The development of polymorphic microsatellite markers will facilitate future ecological and genetic studies involving T. castaneum beetles.
Conservation Genetics Resources, 2013
We report two sets of polymorphic, multiplexed microsatellite markers for the ground beetle Abax parallelepipedus. As the species is flightless, restricted to forests and affected by habitat fragmentation it can serve as a model species for landscape and conservation genetics. A complete set of 20 loci can be amplified in five PCR reactions and sequenced in two rounds, and a subset of 14 loci can be analyzed together in one PCR run and one sequencing round. In a scan of 3,432 individuals from across Germany using the 14 loci subset, we found between three and 14 alleles per locus. After accounting for two loci that are apparently sex-linked, no significant deviations from Hardy-Weinberg equilibrium were found. None of the loci showed evidence for the presence of null alleles. No overall linkage disequilibrium was detected. Some of the loci can also be used to study other Abax species.
Microsatellite flanking region similarities among different loci within insect species
Insect Molecular Biology, 2007
Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements-or their remnants-than unique microsatellite sequences.
Spotted mandarin fish (Siniperca scherzeri Steindachne) feed solely on live fry of other fish species once the fry start feeding in the wild. In the present study, 26 polymorphic transcriptome-derived simple sequence repeat (SSR) markers and 14 genomic SSR markers were developed and characterized in S. scherzeri Steindachne by combining a biotinenrichment protocol and transcriptome of F 1 interspecies hybrids between S. chuatsi (♀) and S. scherzeri (♂). These 40 polymorphic SSRs amplified 168 alleles (mean 4.2). The number of alleles, observed heterozygosity, expected heterozygosity, and polymorphic information content per locus were in the range of 2 to 7 (mean 4.3), 0.1111 to 1.000 (mean 0.6718), 0.3118 to 0.8276 (mean 0.6901), and 0.2735 to 0.7902 (mean 0.6298), respectively. Ten of these microsatellite loci deviated significantly from Hardy-Weinberg equilibrium (P < 0.00125) after Bonferroni correction for multiple tests and no significant linkage disequilibrium (P < 0.00006) was Y.Q. Dou et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 19317-19322 (2015) observed. The microsatellite markers characterized from S. scherzeri could be a valuable tool in genetic evaluation for conservation and for assessment of the mechanism associated with unique food preference of S. scherzeri from a genetic point of view.