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Fig. 1 | Genome Biology

Fig. 1

From: Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

Fig. 1

RagTag enables rapid generation of new reference genomes for the tomato genotypes Sweet-100 and M82. a Images of M82, Micro-tom (MT), and Sweet-100 (S100) plants 44 days (top) and 65 days (bottom) after sowing. Red asterisks indicate open flowers. b Number of inflorescences with open flowers (top), green fruits (middle), and ripe fruits (bottom) at 6 to 9 weeks after sowing. Data points represent individual plants (n=8). c Images of the first developing fruit on M82, MT, and S100 at 65 days after sowing. d Diagram indicating generation times of the M82, MT, and S100 genotypes. e Overview of RagTag “scaffold,” “patch,” and “merge.” f A more detailed diagram describing RagTag “patch”, highlighting how sequence from the query assembly (orange) can be used to fill gaps in the target assembly (green). g A more detailed diagram describing RagTag “merge” showing how each contig is represented by a pair of nodes for the beginning and end termini of the sequence with edges between contigs indicating the pair of contigs are adjacent in one of the candidate scaffolds. The function h() maps contig terminus pairs to Hi-C scores (see Methods section “RagTag “merge””). h nX plots showing the minimum sequence length (y-axis, log scale) needed to constitute a particular percentage of the assembly (x-axis). i Ideogram showing contig boundaries (alternating color and gray) within the final scaffolds. j Circos plots comparing M82 to Heinz 1706 (SL4.0). Circos quantitative tracks a, b, and c are summed in 500 kbp windows and show number of genes (a, lower tick=0, middle tick=47, upper tick=94), LTR retrotransposons (b, 0, 237, 474) and structural variants (c, 0, 24, 48). The inner ribbon track shows whole-genome alignments, with blue indicating forward-strand alignments and red indicating reverse-strand alignments (inversions). Darker colors indicate alignment boundaries. k, As for j but comparing Sweet-100 to Heinz 1706 and showing number of genes (a, 0, 48, 96), LTR retrotransposons (b, 0, 269, 538), and structural variants (c, 0, 30, 59) and whole-genome alignment ribbons. Letters in b represent post hoc Tukey’s HSD tests. Scale bars indicate 10 cm (a) and 1 cm (c)

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