Journal: Cell reports

Article Title: A chromosome-level reference genome and pangenome for barn swallow population genomics

doi: 10.1016/j.celrep.2023.111992

Figure Lengend Snippet: (A) Flowchart of the VGP assembly pipeline 1.6 (redrawn from Rhie et al. ). (B) Genomescope2.0 k -mer profile for bHirRus1 generated from trimmed 10x Linked-Reads, used to estimate genome size, repetitiveness, and heterozygosity (top). The x axis represents multiplicity in the read set, while the y axis represents their cumulative frequency. (C) Merqury spectra-cn plots for bHirRus1. K -mer multiplicity in the 10x Linked-Reads (x axis) versus their frequency (y axis). Colored curves discriminate k -mer occurrences in the assembly. The bar at the origin of the graph represents k -mers found only in the assembly (assembly errors). Two frequency peaks are visible: a haploid peak at ~25× coverage (half average coverage, red), representing k -mers found once in the assembly (haplotype specific), and a diploid peak at ~50× (average coverage, blue) representing k -mers found twice in the assembly (shared between haplotypes). No k -mers resulting from artificial duplications (green, purple, yellow) are visible (duplication content 0.49%; ). (D) Hi-C interaction heatmaps for the curated bHirRus1 assembly. The linear sequence of the reference genome assembly is represented on both axes, and the diagonal shows 3D proximity of interacting pairs. The strength of the interaction is given by color intensity. A scaffold is considered a full chromosome when the number of interchromosomal interactions is negligible. No off-diagonal interactions are visible. Scaffolds are labeled by their chromosome number. (E) Hi-C interaction heatmaps for bHirRus1 assembly before curation. A number of off-diagonal interactions are still visible, which can either result from missing links between scaffolds of the same chromosome or from misassembly. (F) Hi-C interaction heatmaps for Chelidonia assembly. The assembly is still substantially fragmented, with several off-diagonal Hi-C interactions. (G) Snail plots and assembly summary statistics. The main plot is divided into 1,000 size-ordered bins around the circumference. Scaffold length distribution is shown in dark gray with the plot radius scaled to the longest scaffold (red). Orange and pale orange arcs show scaffold N50 and N90, respectively. The pale gray spiral shows the cumulative scaffold count on a log scale, with white scale lines showing successive orders of magnitude. The blue and pale blue areas around the plot show the GC, AT, and N content in the same bins as the inner plot. Top plot: bHirRus1 snail plot. Bottom plot: Chelidonia snail plot. The table summarizes the assembly summary statistics and BUSCO results (vertebrata_odb10) of Chelidonia and bHirRus1. (H) Dotplot alignment of bHirRus1 (blue) and Chelidonia (red) with the VGP chicken assembly GRCg7b. Chromosome numbers and coordinates are reported for GRCg7b (x axis), Chelidonia (y axis, red), and bHirRus1 (y axis, blue). Black vertical lines, red horizontal lines, and blue dashed horizontal lines define chromosome and scaffold boundaries in the chicken assembly, in Chelidonia, and in bHirRus1, respectively. See also and .

Article Snippet: Linked-reads libraries were generated using the 10x Genomics Chromium platform (Genome Library Kit & Gel Bead Kit v2 PN-120258, Genome Chip Kit v2 PN-120257, i7 Multiplex Kit PN-120262) and sequenced on an Illumina NovaSeq S4 150bp PE lane at ~60X coverage.

Techniques: Generated, Hi-C, Sequencing, Labeling

Journal: Cell reports

Article Title: A chromosome-level reference genome and pangenome for barn swallow population genomics

doi: 10.1016/j.celrep.2023.111992

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Linked-reads libraries were generated using the 10x Genomics Chromium platform (Genome Library Kit & Gel Bead Kit v2 PN-120258, Genome Chip Kit v2 PN-120257, i7 Multiplex Kit PN-120262) and sequenced on an Illumina NovaSeq S4 150bp PE lane at ~60X coverage.

Techniques: Recombinant, DNA Extraction, Multiplex Assay, cDNA Synthesis, Amplification, Sequencing, Sample Prep, Generated, Cell Culture, Software