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423 results for “t haplotype”
Multiple mitochondrial haplotypes within individual specimens affect biodiversity estimation by DNA metabarcoding
<p>In the global action for biodiversity conservation, the most urgent need is to delimit and identify species. DNA barcoding and metabarcoding based on molecular markers have been increasingly used in species delimitation and species diversity assessment, respectively, owing to their advantages of standardization and high throughput. The molecular markers used in these methods for animals are mainly derived from mitochondrial DNA. The principle involved is that inter-specific genetic distances are greater than intra-specific genetic distances. However, if multiple mitochondrial haplotypes exist within individual specimens and the divergence between these haplotypes is greater than the assumed maximum intra-specific divergence, the species delimitation and species diversity assessment may be affected. In our recent studies, a widespread phenomenon of multiple mitochondrial haplotypes within individual specimens was discovered in fig wasps (Hymenoptera, Insecta), having negative impact on DNA barcoding and metabarcoding. In this study, we expanded the taxa to include up to 480 specimens from 82 species, 66 genera, 45 families, and 13 orders of Insecta and Arachnida. By high-throughput sequencing of mitochondrial <i>cox1</i> fragments within individual specimens, we studied the pattern of multiple mitochondrial haplotypes within individual specimens. Three DNA metabarcoding strategies, one of which was simulated, were applied. The results revealed that multiple mitochondrial haplotypes within individual specimens could lead to an overestimation of species diversity by metabarcoding. Simultaneously, we found that the infection with intracellular endosymbiotic bacteria <i>Wolbachia</i> was significantly negatively related with this effect. These results suggest that additional attention should be paid to the interference of multiple mitochondrial haplotypes within individual specimens on the results of DNA metabarcoding in species diversity assessment of animals.</p>
Supplementary material 1 from: Gariepy TD, Musolin DL, Konjević A, Karpun NN, Zakharchenko VY, Zhuravleva EN, Tavella L, Bruin A, Haye T (2021) Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia. NeoBiota 68: 53-77. https://doi.org/10.3897/neobiota.68.68915
Table S1. Collection information and GPS coordinates
Methylation haplotypes of the insulin gene promoter in children and adolescents with type 1 diabetes: could a dimensionality reduction approach predict the disease?
<p>The aim of the present study was to identify insulin gene promoter (IGP) methyl-haplotypes among children and adolescents with T1D and suggest a predictive model for the discrimination of cases and controls according to methyl-haplotypes. Fourty individuals (20 T1D) participated. IGP-region from peripheral whole blood DNA of 40 participants (20 T1D) was sequenced by next generation sequencing, sequences were read using FASTQ files, and methylation status was calculated by python-based pipeline for targeted deep bisulfite sequenced amplicons (ampliMethProfiler). Methylation profile at 10 CpG sites proximal to transcription start site of the IGP was recorded and coded as 0 for unmethylation or 1 for methylation. A single read could result in “1111111111” methyl-haplotype (all methylated), “000000000” methyl-haplotype (all unmethylated) or any other combination.</p>
PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza
<p>Modern commercial varieties of tomato (<em>Solanum lycopersicum</em>) are typically F1 hybrids that are genetically heterozygous. Here we generated haplotype-aware assemblies of two different tomato commercial hybrids (Funtelle and Maxeza) using PacBio HiFi reads. The HiFi data was assembled using the Hifiasm assembler allowing for the generation of contigs that distinguish the two parental haplotypes (haplotype-aware assembly). Reference based scaffolding was used to generate the chromosome-scale assemblies available here. It should be noted that although the raw assembly manages to fully distinguish haplotypes we did not test whether the working reference sequence we make available here is fully phased at the chromosome level.</p>
Phase 2 Haplotype Mismatched HSCT in Patients With Hematological Malignancies
ClinicalTrials.gov study NCT00593554. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Biparental HLA Haplotype Disparate T-cell Depleted Transplants for Patients Lacking an HLACompatible Donor
ClinicalTrials.gov study NCT01598025. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Amphibian chytridiomycosis in Japan: distribution, haplotypes, and possible entry into Japan
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Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance
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Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
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Data from: Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity
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Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
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PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza
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Data from: RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
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Data from: Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins
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Data from: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs
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Data from: The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods
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An approach for estimating haplotype diversity from sequences with unequal lengths
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Data from: A likelihood approach for uncovering selective sweep signatures from haplotype data
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Data from: Female house mice avoid fertilization by t haplotype incompatible males in a mate choice experiment
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Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees
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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)
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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.