Journal: Nucleic Acids Research

Article Title: Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

doi: 10.1093/nar/gkac1115

Figure Lengend Snippet: Metrics of the CLR and five HiFi genome assemblies of A. thaliana Ey15-2

Article Snippet: In fact, only very seldom do Bionano DLS optical maps span complete A. thaliana centromeres (1001G + Project).

Techniques:

Journal: Nucleic Acids Research

Article Title: Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

doi: 10.1093/nar/gkac1115

Figure Lengend Snippet: Comparison of different PacBio libraries and assemblers. ( A ) Insert size distribution of the CLR (black) and HiFi (blue) libraries after size-selection on the BluePippin instrument as measured on a Femto Pulse System. ( B ) Contiguity plot comparing the CLR and five HiFi assemblies using the complete dataset. For each assembly, the cumulative contig length (ordered from largest to shortest) is plotted over the estimated genome size of A. thaliana accession Ey15-2 (∼143 Mb). The vertical dashed line indicates the size of the TAIR10 reference genome (119.14 Mb). ( C ) Alignment of the TAIR10 reference genome and the contigs of the CLR and five HiFi assemblies visualized by AliTV . Co-linear horizontal gray bars represent chromosomes or contigs, with sequence annotated as repetitive elements (centromeres, 5S and 45S rDNAs, telomeres, mitochondrial and chloroplast nuclear insertions) indicated by the colors shown on the bottom left. Only Bionano-scaffolded contigs >150 kb are shown. Distance between ticks equals 1 Mb. Colored ribbons connect corresponding regions in the alignment.

Article Snippet: In fact, only very seldom do Bionano DLS optical maps span complete A. thaliana centromeres (1001G + Project).

Techniques: Comparison, Size Selection, Sequencing

Journal: Nucleic Acids Research

Article Title: Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

doi: 10.1093/nar/gkac1115

Figure Lengend Snippet: Hybrid assemblies and features of gaps. ( A ) Contiguity plot comparing the CLR-Canu and HiFi-Hifiasm assemblies alone, combined with RagTag ‘patch’ or as hybrid scaffolds with Bionano optical maps. For each assembly, the cumulative contig—or scaffold—length (ordered from largest to shortest) is plotted over the estimated genome size of A. thaliana accession Ey15-2 (∼143 Mb). The vertical dashed line indicates the size of the TAIR10 reference genome (119.14 Mb). For the assembly that achieved ‘telomere’-to-telomere status (HiFi + optical map), chromosome numbers are indicated on top of the scaffold lines. ( B ) Correlation of gap lengths estimates between Bionano optical maps and CLR ‘patches’ introduced in the HiFi assembly by RagTag . ( C ) Visualization with IGV of aligned HiFi reads (in red; top), subreads from the same HiFi library (in green; middle), and CLRs (in blue; bottom) over Chr5:23640917–23641913, a locus in the HiFi + CLR hybrid assembly ‘patched’ with sequences from the CLR-Canu assembly. ( D ) Zoom out of (C).

Article Snippet: In fact, only very seldom do Bionano DLS optical maps span complete A. thaliana centromeres (1001G + Project).

Techniques:

Journal: Nucleic Acids Research

Article Title: Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

doi: 10.1093/nar/gkac1115

Figure Lengend Snippet: Centromere and 5S rDNA variation between A. thaliana accessions Ey15-2 and Col-0. ( A ) Centromere and ( B ) 5S rDNA length of each chromosome in the HiFi-Hifiasm assembly of accession Ey15-2 and three independent assemblies of accession Col-0: HiFi-Hifiasm in this study, ONT + HiFi in Wang et al. and ONT + HiFi in Naish et al. . ( C ) Comparison of all pericentromeric regions in the HiFi-Hifiasm assemblies of Col-0 and Ey15-2 visualized by StainedGlass . A histogram of the colored percent identity is shown at the top-right of the panel.

Article Snippet: In fact, only very seldom do Bionano DLS optical maps span complete A. thaliana centromeres (1001G + Project).

Techniques: Comparison

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Methylation states in predicted enhancer–promoter pairs. ( A ) schematic illustration of possible methylation states for a promoter and enhancers, and potential interaction between them. ( B ) Bionano Genomics optical methylation map of a region in chromosome 17 in GM12878 DNA. The region contains the gene TP53, its promoter (small blue box), and several predicted enhancers (pink boxes). Dark blue dots denote unmethylated sites and orange dots denote genetic tags used for alignment to the hg38 reference.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of mixtures containing B-lymphocytes and myoblast cells by different methods using methylation states in promoters alone and enhancer–promoter pairs, accounting for one enhancer per promoter. ( A ) Calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) The mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of B-lymphocytes and myoblast cells mixtures by different methods using methylation states in all predicted enhancer–promoter pairs. ( A ) calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) the mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation