Isolation and characterization of 13 polymorphic microsatellites for the Hokkai Shrimp, Pandalus latirostris

We have developed and characterized 13 novel polymorphic microsatellite markers for the Hokkai Shrimp, Pandalus latirostris, to provide an effective tool for conducting genetic studies on this species. No linkage disequilibria and no deviation from HWE were detected in these markers. In 32 individuals from Lake Notoro in Hokkaido, Japan, the number of alleles and expected heterozygosities ranged from 7 to 22 and from 0.84 to 0.95, respectively, suggesting the availability of these markers for ecological studies and conservation genetics in this species.     

Isolation and characterization of 32 polymorphic microsatellites for Xenocypris microlepis

Thirty-two microsatellite markers were isolated from an enriched genomic library of Xenocypris microlepis. Analysis of 40 individuals from a wild population revealed an average of seven alleles per locus, with the range from 4 to 10. The expected and observed heterozygosities ranged from 0.3580 to 0.9467 and from 0.0294 to 0.9474, respectively. Fifteen markers exhibited the deviation from Hardy–Weinberg Equilibrium. All microsatellites were in linkage equilibrium. These newly isolated markers would be useful to study the population genetics and stock management of X. microlepis.     

Isolation and characterization of 8 microsatellites and for the Kea Nestor notabilis

We describe the isolation and characterization of eight polymorphic microsatellite loci for the endemic New Zealand alpine parrot Kea (Nestor notabilis). The loci were initially tested for eight individuals collected across the range and then for a larger dataset of 410 individuals. The number of alleles per loci ranged from 2 to 11. These new microsatellites are useful tools for population studies of this little studied endangered species.     

Isolation and characterization of microsatellites in Portunus trituberculatus

Thirty polymorphic microsatellite markers for swimming crab P. trituberculatus are developed from EST sequences, genomic libraries and cross-species amplification in P. pelagicus, respectively. They are characterized using 24 P. trituberculatus individuals from Yingkou natural population. The number of alleles per locus range from 4 to 21 with a mean number of 10.83. The observed and expected heterozygosities range from 0.250 to 1.000 and from 0.365 to 0.945, respectively. Five loci departed significantly from HWE (P?<?0.05). The genomic-SSRs and EST-SSRs show similar levels of polymorphism for both the average number of alleles (11 alleles vs. 10 alleles) and average PIC values (PIC?=?0.780 vs. PIC?=?0.776). These microsatellite loci from different sources will contribute to improve research on the genetic conservation of P. trituberculatus.     

Isolation and characterization of microsatellites of Grateloupia filicina

Grateloupia filicina has long been considered a textbook example of a marine red alga with a cosmopolitan distribution. It is of important ecological, edible and medicinal values. We isolated 40 new microsatellite DNAs of G. filicina with a modified fast isolation by AFLP of sequences containing repeat protocol and characterized them in 56 individuals collected from Qingdao coast. The number of alleles per locus ranged from 3 to 10. The observed and expected heterozygosities varied between 0.11 and 0.72 and 0.20 and 0.93, respectively. Ten loci deviated from Hardy–Weinberg equilibrium and two loci were at linkage disequilibrium. The microsatellites developed in this study will certainly facilitate the researches on the genetic diversity and differentiation of G. filicina populations.     

Isolation and characterization of 10 polymorphic microsatellites in Meretrix meretrix

Meretrix meretrix is a commercially important bivalve species in China. Due to overfishing for food, the wild stocks are decreasing rapidly. We reported the isolation and characterization of 10 polymorphic loci isolated from apartial genomic DNA library of Meretrix meretrix enriched for CA repeats. A total of 21 primers were designed with online software PRIMER3. We tested variability of these microsatellites on 30 individuals collected in Zhejiang Province. Ten microsatellites were polymorphic. The number of alleles ranged from 2 to 17. The observed heterozygosity was from 0.1667 to 0.9333 and the expected heterozygosity was from 0.1554 to 0.9322. Seven of 10 microsatellites conformed to Hardy–Weinberg equilibrium, and inherited independently. These polymorphic loci provide a valuable tool for assessing population genetic diversity of this species.     

Isolation and characterization of twenty polymorphic microsatellites for Hemibarbus labeo (Cyprinidae)

Conservation Genetics Resources - Hemibarbus labeo is a valuable freshwater fish species distributed in the Heilongjiang River basin in China. Wild resources have declined sharply in recent years...     

Isolation and characterization of 18 microsatellites for Lycengraulis grossidens (Pisces: Clupeiformes)

Twelve polymorphic and six non-polymorphic microsatellite loci were isolated and characterized from a CT–GT enriched genomic library of Lycengraulis grossidens. The number of alleles ranged from 1 to 29. The observed and expected heterozygosity ranged from 0.19 to 0.8 and from 0.18 to 0.95, respectively. Cross-species amplification of the markers developed for L. grossidens was successful in the wild Engraulididae species Anchoa spinifer, Anchoa marinii, Anchoviella lepidentostole, Cetengraulis edentulous and Engraulis anchoita. The developed microsatellite loci are a potential powerful tool for studies of population genetics, genetic diversity and gene flow for these important food sources.     

Isolation and characterization of tetranucleotide microsatellites from the leatherback turtle (Dermochelys coriacea)

The leatherback turtle (Dermochelys coriacea) is a globally endangered marine species. Numerous questions regarding life history and demographics that are of conservation interest remain and many of these can be addressed through the use of highly polymorphic nuclear markers. We describe primers and polymerase chain reaction conditions to amplify 19 tetranucleotide microsatellite loci from the leatherback turtle. The primers were tested on samples from 22 females that nested at Archie Carr National Wildlife Refuge, Melbourne Beach, Florida, USA. The primers developed in this study yielded an average of 9.4 alleles per locus (range of 5–19) and an average observed heterozygosity of 0.84 (range 0.36–1.00). These markers should prove useful in supplementing existing markers for individual and population level analyses.     

Isolation and characterization of eight microsatellites from the South American annual fish Austrolebias charrua

Austrolebias charrua is an endemic annual fish of Uruguay and Brazil. Eight microsatellite markers were developed in order to clarify its population genetic structure. All of them constitute polymorphic loci. The number of observed alleles ranged from 6 to 14, the mean expected heterozygosity from 0.65 to 0.92 and the Shannon-Wiener Diversity Indices from 1.31 to 2.39. This study is the first report of microsatellites in annual killifish and they will be a helpful tool to implement conservation strategies in this endangered species.     

Isolation and characterization of 17 polymorphic microsatellites in the brown mud mussel Glauconome rugosa

The brown mud mussel Glauconome rugosa is a delicious mussel food species. Due to over-harvesting for food in the wild, some populations may be endangered. Seventeen di- and tetranucleotide microsatellites were isolated and characterized using 24 wild caught individuals. The average allele number of the 17 microsatellites was 8/locus with a range of 5–14, and the expected heterozygosity averaged at 0.80, ranging from 0.65 to 0.91. Eleven out of 17 microsatellites agreed with the Hardy–Weinberg equilibrium (HWE) and showed independent segregation. Extreme size difference (over 50 bp) between alleles was seen at five of the 17 loci. These microsatellites will facilitate the studying of the genetic diversity and population structure of wild populations of G. rugosa.     

Isolation and characterization of 8 novel microsatellites for the black abalone, Haliotis cracherodii, a marine gastropod decimated by the withering disease

The black abalone, Haliotis cracherodii, is an intertidal marine gastropod that used to be extremely abundant before overharvesting and an outbreak of withering syndrome lowered its numbers to, in some sites, few individuals. A set of eight microsatellite markers was developed and tested for polymorphism using 41 individuals from two populations. Loci were highly polymorphic with expected heterozygosities ranging from 0.86 to 0.96, a likely signature of past large population size. These markers will be useful in tracking the fate of such a vulnerable species that is likely to experience a severe bottleneck in the next few generations.     

Isolation and characterization of polymorphic microsatellites loci in the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

As one of the major freshwater gastropod species, genetic diversity analysis of Bellamya was totally blank. Fifteen microsatellites loci were isolated and characterized from the freshwater snail Bellamya aeruginosa (Reeve, 1863). Most of the 15 loci had successful amplification and high polymorphic information content value (PIC), which ranged from 0.3174 to 0.8886 (average 0.7074). Allele number per locus ranged from 5 to 12 (average 8.4), the expected heterozygosity (H _E ) and observed heterozygosity (H _O ) varied from 0.6674 to 0.9073 and 0.0714 to 0.9130 with an average of 0.7985 and 0.6779, respectively. Six loci showed significant deviation from Hardy?CWeinberg equilibrium (HWE) after Bonferroni correction (P?<?0.0034) and no significant genotypic linkage disequilibrium was detected between most of locus pair, except for eight locus pairs. These fifteen polymorphic microsatellites loci would be precious for population genetics analysis and species identification of Bellamya.     

Characterization of 12 polymorphic microsatellites for the Reddish Egret, Egretta rufescens

The Reddish Egret is a rare, plumage dimorphic North American heron with disjunct colonies across its range due to habitat specialization. We isolated and characterized 12 novel polymorphic microsatellite loci for the Reddish Egret (Egretta rufescens) using 31 individuals from a single breeding colony in Texas. The number of alleles ranged from 2 to 10 among the loci within the colony. Observed heterozygosity ranged from 0.03 to 0.90 while expected heterozygosity ranged from 0.03 to 0.88. Two loci failed to meet Hardy–Weinberg expectations after correction while none of the loci exhibited significant linkage disequilibrium. Only 1 loci contained possible null alleles. These molecular markers will be used to assess genetic structure across the species range as well as examine potential differentiation between color morphs within and among populations.     

Isolation and characterization of microsatellites in the endoparasitic ichneumonid wasp carrying a polydnavirus Hyposoter didymator

The wasp Hyposoter didymator (Hymenoptera, Ichneumonidae) parasitizes several agricultural pest moths and could therefore be used in biological control. The 454 FLX Titanium pyrosequencing technology was used to define two distinct sets of multiplex combining 14 polymorphic microsatellite loci: 10 (referred to as HD) located within the genome of H. didymator and 4 (referred to as HdIV) located within the Ichnovirus genome which is integrated into the wasp genome. Genotyping of two populations collected in France on Helicoverpa armigera revealed that most of the loci are independent and at Hardy–Weinberg equilibrium.     

Isolation of novel microsatellites for the howler monkey bot fly

The bot fly Cuterebra baeri is a host-specific parasite of howler monkeys (Alouatta spp.). To explore relationships between populations of these taxa on Barro Colorado Island, Panama, we developed 22 microsatellite loci for C. baeri. Twelve of these loci were polymorphic; the mean number of alleles per locus was 3.73 ± 0.3 (range = 2–5), with a mean observed heterozygosity of 0.428 ± 0.052 (range = 0.067–0.683). Overall, variability among the 61 larvae sampled was low, perhaps reflecting the isolation of this island population. Analyses of a subset of these individuals revealed that C. baeri larvae parasitizing the same howler monkey were more closely related to each other than were larvae from different monkeys. Future studies will use these loci to explore such host-parasite relationships in greater detail.     

Isolation and characterization of 25 polymorphic microsatellites of the large Japanese wood mouse (Apodemus speciosus)

The large Japanese wood mouse (Apodemus speciosus) is common, but endemic to Japan, and its population structure was affected by habitat fragmentation because of urbanization. It suggested that the species might be one of the important models for the conservation of ecosystems and biodiversity affected by humans, including the effect of radioactive discharge caused by nuclear power plant accidents at Fukushima. We developed and characterized 25 novel polymorphic microsatellite markers from the next-generation sequencing data in an effort to provide an effective tool for genetic studies on this species. In 8 individuals from Aomori, Japan, the number of alleles and expected heterozygosities ranged from 5 to 13 and from 0.795 to 0.991, respectively, suggesting the availability of these markers for genetic studies in this species.     

Isolation and characterization of polymorphic microsatellites in the perennial herb Euphorbia kansui using paired-end Illumina shotgun sequencing

Euphorbia kansui is a threatened perennial herb endemic to China, and a good knowledge of its population genetics would be essential to the formulation of effective conservation and management strategies. In this study, 12 novel microsatellite markers were developed for E. kansui using Illumina sequencing technology. The number of alleles varied between 2 and 11, with an average of 4.1 alleles per locus. The expected (H _E) and observed heterozygosity (H _O) ranged from 0.0950 to 0.7875 and from 0.0500 to 0.9500, with an average of 0.4050 and 0.4083, respectively. Following the false discovery rate controlling procedure, significant deviations from Hardy–Weinberg equilibrium was only detected in a single locus (Ek1073). These informative microsatellite markers can be readily used for genetic analyses of this threatened plant.     

Isolation and characterization of polymorphic microsatellites in the Tibetan cypress Cupressus gigantea using paired-end Illumina shotgun sequencing

Cupressus gigantea Cheng et L. K. Fu is an endangered conifer endemic to Tibet of China. In this study, 16 polymorphic microsatellite markers were developed using paired-end Illumina shotgun sequencing. The number of alleles varied between 3 and 18, with an average of 8.063 alleles per locus. The observed (H _O) and expected heterozygosities (H _E) ranged from 0.227 to 0.902 and from 0.000 to 1.000, respectively. Following the false discovery rate controlling procedure, six loci showed significant deviations from Hardy–Weinberg equilibrium, and linkage disequilibrium was only detected between a pair of loci. These informative microsatellite markers can be readily used for genetic analyses of this endangered plant.     

Isolation and cross-species characterization of polymorphic microsatellites for the orchid bee Eulaema meriana (Hymenoptera: Apidae: Euglossini)

We describe and characterize eight polymorphic microsatellite loci for the orchid bee species Eulaema meriana, an abundant species and important pollinator in wet lowland forests in tropical America. We also tested the cross-species amplification of these microsatellite loci in seven other species of the genus Eulaema. For E. meriana, number of alleles per locus ranged from four to nine and expected heterozygosity ranged from 0.377 to 0.854. Seven out of the eight loci described amplified in all seven other Eulaema species. These microsatellite loci will be of practical use for population structure, mating system and inbreeding studies in euglossine bees.