Additional file 1 of Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow
Creators: name: Wang, Jianyu
name: Zhang, Lan
name: Wang, Jiaqi
name: Hao, Yanan
name: Xiao, Qimeng
name: Teng, Jia
name: Shen, Shaoqi
name: Zhang, Yan
name: Feng, Yishan
name: Bao, Shoutong
name: Li, Yu
name: Yan, Zimo
name: Wei, Chendan
name: Wang, Li
name: Wang, Jinpeng
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. Genomic comparisons of the studied genomes. a Intergenomic comparison of the V. vinifera and P. trichocarpa genome. b Intergenomic comparison of the V. vinifera and S. brachista genome; c Intragenomic comparison within the P. trichocarpa genome; d Intergenomic comparison of the S. brachista and P. trichocarpa genome. Best-hit genes are represented by red dots and other genes by gray dots. The grape 19 chromosomes colored by 7 eudicot ancestral chromosomes. Genomic syntenic blocks (≥8 gene pairs) inferred from ColinearScan are shown in dotplot according to the genomic locations of V. vinifera, P. trichocarpa, and S. brachista. In a and b, the solid boxes indicate the orthologous regions produced by core-eudicot-common hexaploidization (ECH). In c, the solid boxes indicate the paralogous regions produced by SCT (Salicaceae common tetraploidization event). In d, the solid boxes indicate the orthologous regions between S. brachista and P. trichocarpa. The best paralogy or orthology ratios between studied genomes were 1:2, 1:2, 1:1 and 2:2 in a, b, c and d, respectively. Fig. S2. Intragenomic comparison of the S. brachista genome. The homologous gene dotplot within S. brachista showed the best paralogy ratio of 1:1. Detailed notation and explanation can be found in the legend of Fig. S1. Figure S3. Intragenomic comparison analyses of P.trichocarpa with P. trichocarpa. The best and other matched homologous gene pairs are shown by red and gray dots, respectively. Mean Ks of each inferred colinear blocks are exhibited near their corresponding regions. Fig. S4. Intragenomic comparison analyses of S. brachista with S. brachista. The best and other matched homologous gene pairs are shown by red and gray dots, respectively. Mean Ks of each inferred colinear blocks are exhibited near their corresponding regions. Fig. S5. Intergenomic comparison analyses of P. trichocarpa with S. brachista. The best and other matched homologous gene pairs are shown by red and gray dots, respectively. Mean Ks of each inferred colinear blocks are exhibited near their corresponding regions. Fig. S6. The correction of conversion and density of duplicates in P. trichocarpa. The Y-axis indicatesthe density of duplicated genes (blue lines) and conversion rate (green lines) for selected chromosomes in P. trichocarpa. The X-axis indicates the distance of the duplicated or converted genes from the chromosome termini. Fig. S7. The correction of conversion and density of duplicates in S. brachista. The Y-axis indicates the density of duplicated genes (blue lines) and conversion rate (green lines) for selected chromosomes in S. brachista. The X-axis indicates the distance of the duplicated or converted genes from the chromosome termini.