Fig. 1: Genome and graph pangenome of tomato.
From: Graph pangenome captures missing heritability and empowers tomato breeding
a, Synteny between tomato reference genome build SL4.0 (blue) and SL5.0 (yellow). The grey lines represent synteny blocks. The positions of gaps are marked with black rectangles on the chromosomes, and centromeres are represented by orange rectangles along the chromosomes. b, Contig Nx size of all genome assemblies. SL4.0 and SL5.0 are marked with arrows. Line types represent different sequencing platforms. CLR, PacBio continuous long reads; HiFi, high-fidelity long reads; ONT, Oxford Nanopore long reads. The numbers in parentheses refer to the numbers of assemblies. c, F1 scores (harmonic means of precision and recall) using simulated sequencing data from the genetic variants of 31 accessions with HiFi reads with different depths and genetic variants from the graph pangenome and the linear genome. d, Assessing false-positive (x-axis) and true-positive (y-axis) rates for the graph (Giraffe) and linear (BWA-MEM) mappers using 2,000,000 simulated reads. The size of each point represents the number of reads with mapping quality equal to 60. e, Density map of unique SNPs from SL5.0-332 and TGG1.1-332 located within 1 kb upstream or downstream of the SV breakpoints.
