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Reference genome

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Re-examination of two diatom reference genomes using long-read sequencing

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Mapping our Canu contigs to the reference genome scaffolds indicated that 34 telo- meres on the reference scaffolds were also present on the ends of the homologous Canu contigs. Single telomeres were resolved for 25 of the remaining Flye contigs, which, when mapped to the reference scaf- folds, validated the resolution of the majority of the ‘sin- gle-telomere’ reference scaffolds.

Sketch distance-based clustering of chromosomes for large genome database compression

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A straightforward application of these reference-based compression algorithms to solve the chal- lenging problem of compressing a database containing n number of genome sequences is to conduct a one-by-one sequential reference-based compression for every genome in the database using one fixed reference genome..

Genome sequence of the model rice variety KitaakeX

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Because there are only 219 small variations between KitaakeX and Kitaake (Additional file 8), the KitaakeX genome can also be used as the reference genome for Kitaake.. The de novo assembly of the KitaakeX genome serves as a useful reference genome for the model rice variety Kitaake and will facilitate investigations into the genetic. The day when the first panicle of the plant emerged was recorded as the heading date for that plant..

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

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In the reference genome of IPO323, compartments with these genomic and epigenomic hallmarks represent either accessory chromosomes or specific regions of the core chromosomes. In the genome of the reference Z. tritici strain, the compartments that exhibit the hallmark of accessory chromosomes includes a particular region of the core chromosome 7 of ~ 0.6 Mb (Fig. 3 Genome architecture of the reference genome Z.

Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

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The x-axis represents positions on the reference genome of the MGTV strain Xinjiang2016 (GenBank: MK174251, MK174244, MK174230 and MK174237) and the sRNA-seq data SRR4116826 (Table 1) was aligned to this reference genome. The x-axis represents positions on the reference genome of the MGTV strain Yunnan2016 and the sRNA-seq data SRR8439389, SRR8439390, SRR8432408, SRR8432409, SRR811197093 and SRR811197094 (Table 1) were aligned to this reference genome as negative controls.

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

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Sequencing of the reference genome and mutant isolates The whole genome of the progenitor isolate (11–281) sequenced, assembled and annotated as previously re- ported [49], was used as a reference genome in this study. The genomic DNA samples of the 30 mutant isolates were sequenced using the Illu- mina Hiseq 2000 technology by Novogene Corporation.

Characterization of genome-wide variations induced by gamma-ray radiation in barley using RNA-Seq

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Finally, novel tran- scripts can be detected in transcriptome analysis to im- prove gene annotation of the reference genome.

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

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A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. Genome sequence and genetic diversity of the common carp. Chromosomal-level reference genome of the incense tree Aquilaria sinensis. repeatmasker.org. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. https://doi.org/10.1093/molbev/mst010.. https://doi.org/10.1093/molbev/msy096.

Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

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Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. De novo assembly of the cattle reference genome with single-molecule sequencing. Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle. A whole-genome assembly of the domestic cow, Bos taurus

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

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The basal position of the Basenji makes it useful as a reference for variant ana- lysis as there are clear biases affecting related breeds seen for both the GSD and Boxer reference genomes.. CanFam_Bas offers improved genome contiguity relative to CanFam3.1 and can serve as a representative basal breed in future canid studies. An overview of the China assembly workflow is given in Supplementary Fig.

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

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Location and functional annotation of SNPs and InDels The annotation of the ‘Shuchazao’ reference genome was used to uncover the distribution of SNPs and InDels. According to the gene structure of the reference genome, the overwhelming number of SNPs (94%) was identified in intergenic re- gions, while only of SNPs were located in genic regions (Fig. Similarly, a small pro- portion of InDels were located in the genic regions, which accounted for only of the total num- ber (Fig.

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations

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Metrics based on whole genome alignment to reference genome assembly. genome assembly plots, estimated genome size, datasets and species name for BUSCO analysis and email address to which the plots will be sent.. The gene space completeness analysis of the genome assembly is performed using the BUSCO pack- age version 3.0.2 [8] with genome mode.

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

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The loss of the S. 5 Tree-tracing of the genome-scale similarity across the S. cerevisiae strains from Gallone et al [62] was identified as most similar for a sub-region of the CBS 1483 genome is depicted. n ’ being the total sum of the numxber of times all samples appeared as top-scoring). Moreover, Alpaca leverages previously determined phylogenetic rela- tionships within the reference dataset of strains to infer the evolutionary relationship of the reference genome to the dataset of strains.

Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions

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Here, we used both methods to interrogate the ER2566 genome (Fig. First, we re-sequenced the whole genome of the ER2566 strain grown in our laboratory under consecutive subcul- turing. The raw reads were mapped to the C2566 reference genome (NC_CP014268.2) with a good coverage depth (>. Various de novo assembly softwares were used to construct a confident and long bp) scaffold, and assembly results for each step were assessed by alignment of final sequences back to the reference genome (Fig.

The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population

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Results: Of the CpG sites in the human reference genome, 26.0% show C:G >. T:A substitution in the dataset. Our findings provide insights into the dynamics of the mutation acquisition in the human genome.. (referred to by the pyrimidine of the mutated Watson- Crick base pair) are fixed in one of the two daughter cells and maintained in the descendant cells. First, we investigated the landscape of the C >. T substitutions at the CpGs in all 27,718 CGIs in the human genome.

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

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We calcu- lated the GC content in the 500 kb genomic region around each SNP derived from the Sscrofa 11.1 version of the pig reference genome (http://ensemble.org/Sus_. of the target gene in the test sample. GCG in the test sample. [(mean C t of the target gene in the reference sample. GeneCards (http://www.genecards.org/) and Ensembl (www.ensembl.org/biomart/martview) were used to query gene functions.. org/10.1186/s .

Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica

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Assembly of the HM-1:IMSS clone 6 2001 reference genome. The workflow for genome assembly is shown in a flow diagram [Extended Data 1 (Additional file 1. After scaffolding, we filled in gaps in the assembly using PBjelly. The genome was temporally annotated by Companion.. Additional file 1: Extended Data 1-4.. TKS and SI analyzed and interpreted the genome data.

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

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We then performed fine-mapping of the determined genome-wide associated region using. We filtered CNV calls in the fine- mapped region of association by the mean RD value difference from genomic average (p-value <. 0.001) and the length of the CNV (>. Finally, we discarded all CNV calls overlapping with gaps in the reference genome.. In the individuals with available DNA (n = 101), genotyping of the deletion was performed using a three-primer approach (Fig.

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

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The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance.. The genome of the stress-tolerant wild tomato species Solanum pennellii. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line Δ XT/FT.

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

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is homologous to a se- creted glycoprotein Pry1p of S. obliquus AS-6-11. obliquus AS-6-11, which is the first sequenced self- flocculating microalgal genome, and is also so far the. obliquus AS-6-11 (Table 1) sug- gested its unique feature. obliquus AS-6-11 genome and the lack of S. obliquus AS-6- 11 may serve as a model alga for supplying reference genome annotation and investigating the gene function, evolution, and biotechnology application of S. obliquus AS-6-11 genome than that of Scenedesmus