Additional file 2 of Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance
Creators: name: Cao, Ke
name: Peng, Zhen
name: Zhao, Xing
name: Li, Yong
name: Liu, Kuozhan
name: Arus, Pere
name: Fang, Weichao
name: Chen, Changwen
name: Wang, Xinwei
name: Wu, Jinlong
name: Fei, Zhangjun
name: Wang, Lirong
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 2: Fig. S1. Estimation of genome sizes of P. mira (a), P. davidiana (b), P. kansuensis (c), and P. ferganensis (d) based on K-mer analysis. Fig. S2. Genome size, annotated gene number, and the length of tandam repeat sequences, interpersed repeat sequences in P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Fig. S3. Genome variations across the pseudo-chromosomes of four wild peach species compared to the reference (Prunus persica). The circles from the outer to the inner (A-P) represent copy number variation (CNV) density in P. ferganensis (A), P. kansuensis (B), P. davidiana (C), and P. mira (D), and structure variations (SVs) in P. ferganensis (E), P. kansuensis (F), P. davidiana (G), and P. mira (H), and indels in P. ferganensis (I), P. kansuensis (J), P. davidiana (K), and P. mira (L), as well as SNPs in P. ferganensis (M), P. kansuensis (N), P. davidiana (O), and P. mira (P) in each sliding window of 0.1 Mb. Fig. S4. The electrophoresis results of 20 primers which amplified in two varieties (2010-138 and Shen Zhou Li He Shui Mi) belonging to P. mira (Pm) and P. persica (Pp), respectively. Fig. S5. KEGG pathways enriched in genes comprising large-effect SNPs of between P. ferganensis and P. persica. Fig. S6. KEGG pathways enriched in genes comprising indels in four wild peach species compared to P. persica. Fig. S7. KEGG pathways enriched in genes comprising structure variations in P. mira and P. kansuensiss compared to P. persica. Fig. S8. KEGG pathways enriched in genes comprising copy number variations in P. ferganensis (a), P. kansuensis (b), P. davidiana (c), and P. mira (d) compared to P. persica. Fig. S9. Venn diagram of gene families identified from the five species of peach. Fig. S10. Statistics of single-copy orthologs, multiple-copy orthologs, and unique orthologs in 15 species. Fig. S11. KEGG pathways enriched in expanded and contracted gene families of the four wild peach species. Fig. S12. Whole-genome duplication and speciation events in peach as revealed by the distribution of 4DTv distance among paralogous and orthologs genes in different species. Fig. S13. Distribution of resistance (R) genes across the 8 chromosomes in five peach species of peach and their overlaps with disease resistance QTLs. Fig. S14. Percent of P. davidiana-specific contigs covered by reads from different Prunus species. Fig. S15. Collinearity among P. davidiana, P. mira, P. dulcis, P. armeniaca, and P. avium genomes. Fig. S16. Geographical distribution of P. mira (red circle), P. davidiana (yellow), and P. dulcis (orange) which originated in China. Fig. S17 .Expression of 19 R genes in two accessions (‘Hong Gen Gan Su Tao 1#’ and ‘Bailey’) inoculated with nematode after 0, 6, 12, 36, 60, and 84 hours. Fig. S18. The evaluation of resistant to root-knot nematodes in transgenic tomato lines with Prupe.2G053600 gene and its wild type. Fig. S19. The vector construction (a) and promoter activity assay (b) of Prupe.2G253600 promoter which recovered 35 bp deletion in ‘Hong Gen Gan Su Tao 1#’ peach. Fig. S20. The altitude distribution of accessions used to identify altitude adaptability related genes for genome resequencing. Fig. S21. Phylogenetic tree of 32 accessions of P. mira (a) originating from regions with different altitudes (b) and the population structure (c) when K=2 and 3. Fig. S22. Two genome regions associated with high-altitude adaptation. Fig. S23. The gene expression of wild-type (WT) and three transgenic plants (OE1-OE3) in Arabidopsis which induced by 4 °C for different period. Fig. S24. The proline content of wild-type (WT) and transgenic plant (OE) in Arabidopsis which induced by 4 °C for 24 and 48 hours. Fig. S25. A deletion identified in the promoter of Pmi02g3025 gene in varieties with different altitude.