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Circos plot of the <t>Hypomesus</t> <t>nipponensis</t> genome, with lines of different colors in the diagram represent the colinearity within the genome. The rings from inside to outside indicate (a) pseudochromosome length of the Hypomesus nipponensis genome (b) GC density (c) TE density, and (d) gene density; b-d were drawn in 100-kb sliding windows.
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Circos plot of the Hypomesus nipponensis genome, with lines of different colors in the diagram represent the colinearity within the genome. The rings from inside to outside indicate (a) pseudochromosome length of the Hypomesus nipponensis genome (b) GC density (c) TE density, and (d) gene density; b-d were drawn in 100-kb sliding windows.

Journal: Frontiers in Genetics

Article Title: Chromosome-level draft genome assembly of Hypomesus nipponensis reveals transposable element expansion reshaping the genome structure

doi: 10.3389/fgene.2025.1502681

Figure Lengend Snippet: Circos plot of the Hypomesus nipponensis genome, with lines of different colors in the diagram represent the colinearity within the genome. The rings from inside to outside indicate (a) pseudochromosome length of the Hypomesus nipponensis genome (b) GC density (c) TE density, and (d) gene density; b-d were drawn in 100-kb sliding windows.

Article Snippet: Hypomesus nipponensis muscle sample was collected from the Yalu River in Dandong (N 40.51, E 124.97), China, for whole genome sequencing.

Techniques:

(A) Gene family analysis and divergence time of ten representative species, gray lines indicate confidence intervals. (B) The distribution of the synonymous substitution rates (Ks) of homologous genes between Esox lucius and Hypomesus nipponensis , O. eperlanus and Hypomesus nipponensis , Hypomesus transpacificus and Hypomesus nipponensis , P. chinensis and Hypomesus nipponensis . (C) Shows GO enrichment for expanded gene families. (D) shows GO enrichment for contracted.

Journal: Frontiers in Genetics

Article Title: Chromosome-level draft genome assembly of Hypomesus nipponensis reveals transposable element expansion reshaping the genome structure

doi: 10.3389/fgene.2025.1502681

Figure Lengend Snippet: (A) Gene family analysis and divergence time of ten representative species, gray lines indicate confidence intervals. (B) The distribution of the synonymous substitution rates (Ks) of homologous genes between Esox lucius and Hypomesus nipponensis , O. eperlanus and Hypomesus nipponensis , Hypomesus transpacificus and Hypomesus nipponensis , P. chinensis and Hypomesus nipponensis . (C) Shows GO enrichment for expanded gene families. (D) shows GO enrichment for contracted.

Article Snippet: Hypomesus nipponensis muscle sample was collected from the Yalu River in Dandong (N 40.51, E 124.97), China, for whole genome sequencing.

Techniques:

(A) The number of tandem repeat sequences of different lengths in H. nippomensis , Gasterosteus aculeatus and Tetraodontidae . (B) Transposable element (TE) accumulation history in the Hypomesus nipponensis genome, based on a Kimura distance-based copy divergence analysis of TEs, with Kimura substitution level (CpG adjusted) illustrated on the x-axis, and percentage of the genome represented by each repeat type on the y-axis. The bar color indicates the repeat type. (C) HiFi reads the coverage depth of three scattered sequences. (D) Heatmap of average nucleotide identities between pairwise combinations of genomic intervals from three sequences.

Journal: Frontiers in Genetics

Article Title: Chromosome-level draft genome assembly of Hypomesus nipponensis reveals transposable element expansion reshaping the genome structure

doi: 10.3389/fgene.2025.1502681

Figure Lengend Snippet: (A) The number of tandem repeat sequences of different lengths in H. nippomensis , Gasterosteus aculeatus and Tetraodontidae . (B) Transposable element (TE) accumulation history in the Hypomesus nipponensis genome, based on a Kimura distance-based copy divergence analysis of TEs, with Kimura substitution level (CpG adjusted) illustrated on the x-axis, and percentage of the genome represented by each repeat type on the y-axis. The bar color indicates the repeat type. (C) HiFi reads the coverage depth of three scattered sequences. (D) Heatmap of average nucleotide identities between pairwise combinations of genomic intervals from three sequences.

Article Snippet: Hypomesus nipponensis muscle sample was collected from the Yalu River in Dandong (N 40.51, E 124.97), China, for whole genome sequencing.

Techniques:

(A) Ancestral karyotype and chromosomal evolution of various Salmoninae species. (B) Collinearity analysis of Hypomesus nipponensis , Esox lucius , and O. eperlanus genomes.

Journal: Frontiers in Genetics

Article Title: Chromosome-level draft genome assembly of Hypomesus nipponensis reveals transposable element expansion reshaping the genome structure

doi: 10.3389/fgene.2025.1502681

Figure Lengend Snippet: (A) Ancestral karyotype and chromosomal evolution of various Salmoninae species. (B) Collinearity analysis of Hypomesus nipponensis , Esox lucius , and O. eperlanus genomes.

Article Snippet: Hypomesus nipponensis muscle sample was collected from the Yalu River in Dandong (N 40.51, E 124.97), China, for whole genome sequencing.

Techniques: