Lessons from a beetle and an ant: coping with taxon-dependent differences in microsatellite development success (original) (raw)
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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.
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.
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.
European Journal of Entomology, 2011
Currently it remains difficult to obtain robust microsatellite markers for Lepidoptera. In an attempt to overcome the problems associated with developing microsatellite markers for this insect order we combined (i) biotin-enrichment protocol, (ii) next generation pyrosequencing (through 454 GS-FLX Titanium technology) and (iii) the use of individuals collected from eight geographically distant European populations representing three subspecies of Euphydryas aurinia. Out of 96 stringently designed primer pairs, 12 polymorphic microsatellite loci amplified without obvious evidence of null alleles in eight individuals from different subspecies. Between five and seven of these loci showed full within population applicability and three revealed to be robust and transferable between populations and sub-species, providing a first step towards the development of a valuable and robust tool for studying conservation issues and evolution in E. aurinia populations. Nevertheless, as in most studies dealing with Lepidoptera microsatellites, null alleles were detected in most of the developed markers. Our results emphasize the need for further research in order to better understand the complex evolution and organization of Lepidopteran genomes.
Microsatellite Markers in Plants and Insects. Part I: Applications of Biotechnology
Biotechnology is integral to the application of robust, high through-put detection of species-specific and species or genus-transferred microsatellites, or simple sequence repeat (SSR) markers. These short, tandemly repeated stretches of DNA of variable motifs and lengths are relatively evenly distributed throughout eukaryotic nuclear, chloroplasts, and mitochondrial genomes. Microsatellites are inherited as Mendelian co-dominant markers that provide insights into non-Mendelian inheritance such as microsatellite evolution, replication, repair, recombination, and mutation. These characteristics have made microsatellites the genetic marker of choice for most technologically-driven applications in plant and insect genetic studies such as mapping, marker-assisted selection (MAS), and genetic diversity studies. MAS and linkage mapping analyses has greatly assisted breeding programs through the discovery and isolation of many important agronomic genes that underlie respective phenotypes. Linkage maps and genome sequences have provided comparative genomic insights in plants and insects regarding microsatellite distribution, occurrence, and adaptive phenotypic evolution. Furthermore, genomic synteny and SSR sequence conservation have not only provided maximum annotated information for model plants and insects, but have demonstrated cross-species/genera transferability, which is indicative of long evolutionary history. It is the aim of this paper, therefore, to review biotechnology platforms and applications that have made SSR markers so useful as well as to discuss the impact of SSR transferability across species and/or genera.
Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle
Journal of Heredity, 2008
Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F IS , F ST , population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.
Polymorphic microsatellite markers for the ant Plagiolepis pygmaea
Detailed studies on kin structure, mating patterns and dispersal in social insects require highly polymorphic markers, of which the most commonly used today are DNA microsatellites. Here we characterize 10 polymorphic microsatellite markers for the ant Plagiolepis pygmaea . We also investigated the within-genus applicability of the markers on P. xene , a social parasite of the source species. In addition, we tested amplification of the markers in three species of the genera Formica and Lasius . Eight of the markers also amplified in P. xene and were polymorphic. Seven markers amplified in at least one other formicine ant.
Bulletin of Entomological Research, 2011
The analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.
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.