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Whole-genome

Tìm thấy 14+ kết quả cho từ khóa "Whole-genome"

Population analysis of the Korean native duck using whole-genome sequencing data

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Although some recent stud- ies have investigated the unique characteristics of the Korean native duck [17–20], whole genome-level studies for the Korean native duck still lag behind other domes- tic animals and duck breeds.. To address this, we apply a population-level genome ana- lysis based on whole-genome sequencing data from popula- tions of various duck breeds including KD.

Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

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Genome-wide analysis of DNA methylation profiles on sheep ovaries associated with prolificacy using whole-genome bisulfite sequencing. Relationship between DLK1 gene promoter region DNA methylation and non-small cell lung cancer biological behavior. Parent-of- origin DNA methylation dynamics during mouse development.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

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pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data. Background: Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Results: To offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data.

Multi-trait GWAS using imputed highdensity genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

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Multi-trait GWAS using imputed high- density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia. Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species.

Comparative whole-genome and proteomics analyses of the next seed bank and the original master seed bank of MucoRice-CTB 51A line, a rice-based oral cholera vaccine

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We have not performed genome-wide gene expression profiling for the seed bank, but we have compared the genic regions of the chromosomes in NSB and MSB samples by examining whole-genome sequence datasets..

Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

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The highly differentiated windows based on whole-genome SNPs. The distribution of the highly differentiated SNPs.. The highly differentiated regions based on INDELs between PPD affected and normal pigs. Plots of whole-genome screening of puta- tively loci which associated with PPD in the large family. (B) F ST plot of the whole selected SNPs between 3 affected and normal individuals. (C) F ST plot between the 3 affected and normal individuals based on whole selected INDELs.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

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However, the whole-genome sequencing of Siberian musk deer has not been performed, and their potential value has yet to be discovered.. In this study, we perform high-quality whole-genome sequencing of three wild Siberian musk deer (WSMD) from Mongolia, and transcriptome sequencing of one mixture of tissue from a naturally died female WSMD..

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

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Genotypic drug resistance using whole-genome sequencing of mycobacterium tuberculosis clinical isolates from North-Western Tanzania. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

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Whitacre et al. detected 13 genes potentially in- volved in the development of the hindlimbs based on the whole genome sequence of buffalo [9]. In the current study, the fixation index (Fst) was used to meas- ure the genetic differentiation between populations [10].. The larger Fst value indicates the difference in the two populations. Rubin et al. In the present study, 27 whole genomes of buffalo (in- cluding 15 newly sequenced FZ buffalo genomes and 12.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

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Whole-genome

Whole-genome resequencing using nextgeneration and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741

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In this study, we performed whole-genome resequencing of transgenic poplar 741 using NGS and Nanopore sequencing, and analyzed the copy number and insertion sites of the T-DNA as well as the flanking sequences at the T-DNA integration site. After performing quality-control checks, a total of 52.3 million clean reads for transgenic poplar 741 line Pb29 were obtained from the raw reads, corre- sponding to more than 30× coverage of the Populus trichocarpa reference genome (https://www.ncbi.nlm..

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

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Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. A Survey of Copy Number Variation in the Porcine Genome Detected From Whole- Genome Sequence. A large interactive visual database of copy number variants discovered in taurine cattle. Global variation in copy number in the human genome.

Comparative genomics of whole-cell pertussis vaccine strains from India

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Short-read whole-genome sequencing for laboratory-based surveillance of Bordetella pertussis. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing. Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains.

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

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A whole- genome assembly of the domestic cow. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, et al.. Loh PR, Danecek P, Palamara PF, Fuchsberger C, Reshef YA, Finucane HK, et al

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks

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In the genome of S. a Species identification based on whole genome average nucleotide identity (ANI). b Species identification based whole genome using rMLST. c Species identification based whole genome using TYGS. In the genome of E. 90%) were found in the genomes of nine isolates (Fig. 4), suggesting that IS6 and IS3 contribute in the transfer of these virulence factors. In the genome of L..

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

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These RADseq and reduced representational approaches assess only a limited portion of the genome, and may miss many markers, particularly in species with small sex- specific domains or those with micro-sex chromosomes [47].. The species has heteromorphic XY sex chromosomes [57]. duperreyi to apply an in silico whole genome subtraction approach, and de- velop new practical markers, useful in ongoing studies of this species in the laboratory and the wild.. In silico whole genome subtraction.

Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

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To conduct whole genome comparisons, one pathogenic Fo koae isolate (44) and one non-pathogenic Fo isolate (170) were whole genome sequenced using Illumina TruSeq short-read sequencing (150 bp). Libraries re- sulted in reads with 1245x coverage for pathogenic isolate Fo koae 44 and reads with 1150x coverage for non-pathogenic isolate Fo 170.. De novo assembly of both Fo koae 44 and Fo 170 identi- fied genome sizes of 48 and 50 Mb, respectfully.

Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

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Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies.

Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

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DB and DV conducted the genome sequencing and assembly of the raw data. AVDE and YP provided initial annotation of the sequence. DL and ML conducted the typing analyses, whole genome phylogenetic analyses of the chromosome and plasmid, and. Emended description of the order Chlamydiales, proposal of ParaChlamydiaceae fam.

Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

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Whole genome comparisons reveal panmixia among fall armyworm. Background: The fall armyworm (Spodoptera frugiperda (J.E. 80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain).