Skip to main content
Fig. 1 | Genome Biology

Fig. 1

From: A pan-Zea genome map for enhancing maize improvement

Fig. 1

Pan-Zea genome, gene, orthologous group PAV, and variant graph genome representation. A The genomic landscape of the pan-Zea genome. The pan-Zea genome (PANZ) comprised the AGPv4 reference genomes (RefChr_1–10) and non-reference sequences (NRINS_1–10 and NRINS_Unanchored_1–4). The reference sequence did not belong to the 10 chromosomes and the related anchored non-reference sequences were not plotted. See the legend in the circle diagram for details. B Proportions of different assembly types in the anchored non-reference sequences. “Chromosome-level assembly only”, non-reference sequences that were only found in the 11 chromosome-level genome assemblies; “Re-sequence assembly only”, non-reference sequences that were only found in the 721 WGS de novo assemblies. C Proportion of anchored non-reference sequences with different sub-group origins. TEO, LAND, and MZ represent teosinte, landrace, and modern maize origins, respectively. D Comparison of non-reference sequences from this study to those generated from the founders of maize nested association mapping population (NAM founder). E Sankey plot of the proportions of the core and dispensable genes in pan-Zea (PANZ), the teosinte sub-group (TEO), and the maize sub-group. F Distribution of the number of pan (black) and core (blue) genes along with different numbers of sequenced individuals. See also Additional file 1: Fig. S8D–E. G Schematic of the variant graph genome representation for AGPv4 Chr2:171064-171220, with the SNP paths, short InDels, and a large deletion. H The identity and mapping rate distribution of the simulated short reads from the genomes of the 26 NAM founders against the variant graph. Dark blue individuals are presented on the variant graph, whereas light blue individuals are not

Back to article page