Table 1.
Comparison of assembled genomes between ‘Junzao’ and ‘Dongzao’
Fig 1.
Evolutionary scenario of genome rearrangements from the ancestor of Rosales to jujube, peach and apple.
In the top-right diagram, different colors in each chromosome represent the origin from the seven common ancestral chromosomes of eudicot, and the eight chromosomes filled with different colors represent putative paleo-chromosomes for the common ancestor of Rhamnaceae and Rosaceae.
Fig 2.
(A) Neighbor-joining phylogenetic tree of jujube accessions based on whole-genome SNP data. The jujube accessions are marked with E (east) or W (west), indicating their geographical distributions. (B) PCA of cultivated and wild jujube populations using whole-genome SNP data. (C) Population structure analysis of jujube accessions using FRAPPE at multiple kinship levels (K = 2, 3, 4 and 5). Each vertical bar represents one jujube accession. The length of each colored segment in each vertical bar represents the proportion contributed by ancestral populations. The accession marked with * in part A corresponds to the wild jujube ‘Yanchuandasuanzao’.
Fig 3.
Jujube sugar and acid metabolism associated with domestication.
(A) Sugar and acid accumulation in fruits at various developmental stages from cultivated and wild jujubes. YF, young fruit; EF, expanding fruit; WMF, white mature fruit; HRF, half-red fruit; and FRF, full-red fruit. (B) Number of genes detected in the putative selective regions using different methods. (C) Transcript abundance of genes involved in sugar and acid metabolism in cultivated and wild jujubes. Stars indicate the genes that were located in the regions putatively detected as selective sweeps. Scaled log2 expression values (RPKM) are shown in the heat map legend. The six boxes in one row of each heat map (left to right) correspond to the expression levels at stages EF, HRF and FRF of the wild accession (‘Qingjiansuanzao’) and WMF, HRF and FRF of the ‘Junzao’ cultivar. Each row in the heat map corresponds to one gene. SUSY: sucrose synthase; SPS: sucrose phosphate synthase; SPP: sucrose-phosphatase; HK: hexokinase; FK: fructokinase; PK: pyruvate kinase; MDH: malate dehydrogenase; ACO: aconitate hydratase; IDH: isocitrate dehydrogenase; SDH: succinate dehydrogenase; CS: citrate synthesis; NINV: neutral invertase; CWINV: cell wall invertase; vAINV: vacuolar acid invertase; PFK: 6-phosphofructokinase.
Fig 4.
Characterization of the jujube S locus.
(A) Phylogenetic analysis of three T2-RNase sequences from each ‘Junzao’ (Zj.jz) and ‘Dongzao’ (Zj.dz) with other known S genes. (B) Expression (RPKM) of S-RNase and S-like RNase genes in different tissues. (C) Physical positions of S-RNase and SFB genes on chromosome 1 of the ‘Junzao’ genome. The scaled log2 expression values (RPKM) are shown in the heat map. From left to right, leaf (L), flower (F), phloem (P), expanding fruit (EF), half-red fruit (HR) and full-red fruit (FR). (D) Frequency of S-locus genotypes in 32 jujube accessions.