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135 results for “microsatellite marker”
Data from: Stay at home aphids: comparative spatial and seasonal metapopulation structure and dynamics of two specialist tansy aphid species studied using microsatellite markers
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Data from: Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo)
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Data from: Isolation, characterization, and cross-amplification of 20 microsatellite markers for the rare Conospermum undulatum (Proteaceae)
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Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
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Data from: Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)
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Data from: Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations
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Data from: Development and characterization of 15 polymorphic di-nucleotide microsatellite markers for tule elk using HiSeq3000
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Data from: A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird
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Data from: Genetic diversity and population structure of three traditional horse breeds of Bhutan based on 29 DNA microsatellite markers
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Data from: Multiplexed microsatellite markers for genetic studies of beech
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Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds
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Data from: Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers
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Data from: Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.
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Data from: Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
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Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
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Data from: De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing.
Recent developments in sequencing technologies and bioinformatics analyses provide an unprecedented opportunity for cost and time effective high quality microsatellite marker discovery in non-model organisms for which no genomic information is available. Here, we use shotgun pyrosequencing of a microsatellite-enriched library to develop, for the first time, microsatellite markers for Alnus glutinosa, a keystone tree species of European riparian woodland communities. From a total of 17,855 short sequences, we identified 590 perfect microsatellites from which 392 had designed primers. A subset of 48 loci were tested for amplification, twelve of which were polymorphic in A. glutinosa. These twelve loci were successfully co-amplified in a single multiplex PCR experiment and validated for population genetics applications. In addition, ten and eight of these microsatellites were found to be transferable to the related A. incana and A. cordata species. The developed multiplex of 12 microsatellite markers therefore provides new opportunities for experimental evolutionary and forest genetics research in Alnus.
New set of microsatellite markers for the great-billed seed-finch (Sporophila maximiliani – Passeriformes: Thraupidae): tools for inspection and conservation
<p>The Thraupidae family is one of the most wanted by bird breeders in Brazil due to its diverse, colorful and melodious singers as representatives. The Great-billed Seed-finch, Sporophila maximiliani, is the only representative of the genus Sporophila considered critically endangered in Brazil. Due to the demands of environmental agencies and of conservation programs, there is a need to increase the number of molecular markers available for the genus and specially for S.maximiliani. Therefore, this work aimed to provide a new set of microsatellite markers for S. maximiliani in order to help bird breeders and environmental agencies on fulfilling its demands as well as contributing with extra genetics tools for conservation programs of the Great-billed Seed-finch. Of the 30 markers developed, 25 successfully amplified and 22 were polymorphic. Annealing temperature varied from 52 to 64°C, number of alleles from two to 13 and the medium allele richness was 7.25 and medium expected and observed heterozygosity was, respectively, 0.812 and 0.661. The identity estimate was 8.54x10 -27 and all the other probabilities of non-exclusion (sib-identity, parent pair and first-parent) were <0.001, indicating that this set of microsatellite markers have high genetic variability and high power of individual genetic differentiation for S.maximiliani. Therefore, this work increases the options of molecular markers to be used on inspection for environmental agencies and for conservation programs on analyzing genetic variability and population studies for the Great-billed Seed-finch.</p>
Data from: Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae)
Background: Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. Results: Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9,563 contigs. A total of 4,510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2,389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6,911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from -0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. Conclusions: The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability.
Data from: Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia)
Comparative ecological and behavioural studies of the widespread and diverse Vespertilionidae, which comprise almost 400 of the 1,100 bat species, have been limited by the availability of markers. The potential of new methods for developing conserved microsatellite markers which possess enhanced cross-species utility has recently been illustrated in studies of birds. We have applied these methods to develop enhanced microsatellite markers for vespertilionid bats, in particular for the genus Myotis (103 species). We compared published bat microsatellites with their homologs in the genome sequence of the little brown bat, Myotis lucifugus to create consensus sequences which were used to design candidate primer sets. Primer sets were then tested for amplification and polymorphism in 22 species of bat from nine of the largest families (including 11 Vespertilionidae). Of 46 loci tested, 33 were polymorphic, on average, for each of seven Myotis species tested, 20 in each of four non-Myotis vespertilionid species, and two in 11 non-vespertilionid species.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.