Isolation and Characterization of Nine Microsatellite Loci from the Hawaiian Grouper Epinephelus Quernus (Serranidae) for Population Genetic Analyses (original) (raw)
Related papers
Isolation and characterization of nine microsatellite loci for the takin (Budorcas taxicolor)
Conservation Genetics, 2008
The sycamore lace bug, Corythucha ciliata (Say) (Hemiptera: Tingididae) of North America, is an invasive pest of plane and sycamore trees (Platanus spp.) (Proteales: Plantanaceae), and has invaded many countries. To explore the population genetic structure and the invasion route by which C. ciliata reached China, we developed 9 highly polymorphic microsatellites loci by the FIASCO method. Polymorphism of the 9 loci was assessed in 48 individuals from 2 populations (Guiyang and Nanjing) in China. The number of alleles per locus ranged from 2 to 13. The observed (H O) and expected (H E) heterozygosities varied from 0.146 to 0.958 and 0.290 to 0.849, respectively, in Guiyang population. Likewise H O and H E varied from 0.483 to 0.739 and 0.443 to 0.865, respectively, in Nanjing population. Two loci (CA15 and GA365) showed significant deviations from the Hardy-Weinberg equilibrium (HWE) in Nanjing population. Moreover, loci CA200>26, GT26&TG100, and TG100&GA365 showed significant linkage disequilibria (LD) in the Guiyang population (P < 0.01), and loci GT26 and GA5 (P < 0.01) showed significant linkage disequilibria (LD) in the Nanjing population. Finally, we found 2 types of mutational events that could generate the new alleles, but the main mutation mechanism for the newly developed microsatellites was slippage in the repeat motif and in the flanking region. In future work, the nine loci identified here will be used to study the population genetic structures of C. ciliata populations in China and in putative regions of their origin, and investigate the probable route by which the pest reached China.
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.
Insects
The sycamore lace bug (Corythucha ciliata Say, 1832) is of North American origin, but after its introduction to Europe (1964), South America (1985), Asia (1995), Australia (2006), and Africa (2014), it became an abundant and widespread pest on plane (Platanus spp.) trees. We analysed a 1356 bp long fragment of the mtDNA (COI gene) of 327 sycamore lace bug individuals from 38 geographic locations from Europe, Asia, and North America. Seventeen haplotypes (17 HTs) were detected. C. ciliata populations from North America exhibited higher haplotype diversity (12 HTs) than populations from Europe (6 HTs), Asia (4 HTs), or Japan (2 HTs). The haplotypes formed two haplogroups separated by at least seven mutation steps. One of these mutation steps includes HTs from North America and Japan. Another includes HTs from North America, Europe, and Asia. Haplotypes from Asia Minor, the Caucasus, and Central Asia are linked to haplotypes from Europe, while haplotypes found in Japan are linked to ha...
Journal of Stored Products Research, 2016
The rice weevil, Sitophilus oryzae is one of the primary pests of stored grains worldwide. To develop and implement an effective integrated pest management strategy, an understanding of the population structuring of this destructive pest is vital. In this study we used Illumina paired-end sequencing to develop S. oryzae species-specific microsatellite markers, and used these markers to conduct a preliminary assessment of population structuring in four populations of S. oryzae from three countries (Australia, China, and USA). 7,635,996 raw sequencing reads were produced, with 11,794 microsatellites detected and 214,257 primer options designed. 48 microsatellite markers were selected for further validation, with 10 markers amplifying consistently across the four S. oryzae populations. These markers displayed a high level of polymorphism overall (6.67 alleles/locus), though this was slightly lower within populations (3.10-4.88 alleles/locus). We used the markers to conduct a preliminary assessment of genetic structuring among the four S. oryzae populations: three laboratory cultures (New South Wales, Queensland, and Santai) and a field collected population from Kansas. Analyses suggest high levels of genetic differentiation between the sample locations, with a global F ST of 0.239, and pairwise F ST values ranging from 0.100 to 0.395. Bayesian clustering analyses suggest these four populations formed four distinct clusters, with a similar pattern identified by Principal Coordinate Analysis. These microsatellite markers, together with our preliminary population genetic analyses, will provide a valuable resource for population genetic research, and contribute to effective integrated pest management strategies in the future.
Proceedings of The 1st International Electronic Conference on Entomology, 2021
The sycamore lace bug (SLB) (Corythucha ciliata) is one of the most abundant and widespread pests on plane (Platanus spp.) trees. 38 geographic location of C. ciliata from Europe, Asia and North America were analysed by sequencing. Seventeen haplotypes were detected on 1356 bp long fragment of the COI gene from 327 individuals. C. ciliata populations from North America showed a higher haplotype diversity (12 HTs), than populations from Europe (6 HTs) or populations from Japan (2HTs). The haplotypes formed two haplogroups, one including only North American HTs and another one including HTs from all continents.
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.
Molecular Ecology Notes, 2002
We describe the isolation of six polymorphic microsatellites for Cicada barbara (Stål), four of which are also polymorphic for the closely related Cicada orni L. Cicadas from several sites in the Iberian Peninsula, North Africa (C. barbara) and Greece (C. orni) were genotyped at these loci. Polymorphism is higher than that previously obtained with allozymes for these species. One locus allows species diagnosis (nonoverlapping allele size ranges) between C. barbara and C. orni and the others have some exclusive alleles for each species.
Nucleic Acids Research, 1993
A set of 52 (CT)n and 23 (GT)n microsatellites in honeybee, 24 (CT)n and 2 (GT)n microsatellites in bumblebee (n >6) have been isolated from partial genomic librairies and sequenced. On average, (CT)n and (GT)n microsatellites occur every 15 kb and 34 kb in honeybee and every 40 kb and 500 kb in bumble-bee, respectively. The prevailing categories are imperfect repeats for (CT)n microsatellites in bumble-bee, and perfect repeats for both (CT)n and (GT)n microsatellites in honey-bee. Comparisons with data available in vertebrates indicate a lower proportion of perfect repeats in bees but length distributions are very similar regardless the phylum. This result extends to insects the concept of an evolutionary conservation for quantitative and qualitative characteristics of (CT)n and (GT)n microsatellites. Many (CT)n and (GT)n repeats are surrounded with various types of microsatellites, revealing an associative distribution of short repeat sequences. As expected, a high level of intrapopulational polymorphism has been found with one tested honeybee microsatellite. Also, flanking regions of this microsatellite are similar enough to allow PCR amplification in several other species of Apis and Bombus.