Additional file 2 of RXLR effector genes mediate regional adaptation of Phytophthora infestans
Creators: name: Zheng, Jie
name: Tian, Peng
name: Li, Wanyue
name: Cao, Yimeng
name: Meng, Yuling
name: Zhan, Jiasui
name: Shan, Weixing
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 2: Figure S1. Genotyping of P. infestans by five (SSR4, SSR6, SSR8, Pi4B, and Pi02) SSR markers. a Cluster graph based on P. infestans genotype. b Proportion of each P. infestans genotype in TSGS and WNGZ populations. Different colors represent different genotypes, and the dominant genotypes are marked with blue and red. Figure S2. Genetic structure and diversification of P. infestans populations in TSGS and WNGZ. a Phylogenetic tree of 19 isolates based on population SNPs. Blue and red represent the isolates from TSGS and WNGZ, respectively. b PCA analysis of two populations. c Distribution of Fst along the supercontigs of the genome. The value of Fst ranged from 0–1. 0 indicates a completely consistent genetic locus, and 1 indicates that alleles are fixed in different populations. d Comparison of pair-wise SNP abundance among isolates with different classification groups. Statistical significance was assessed by Student’s t-test. ns, not significant. *** P &lt; 0.001. e Phylogenetic tree of isolates based on haplotypes at RXLR effector genes. Figure S3. Sequence variation features of RXLR effector genes. a, b Number of SNPs (left) and InDels (right) in coding regions and promoter regions of effector genes in each isolate. The number above the black line represents the union of SNPs and InDels of all isolates from the same region. c, d Number and distribution of regional specific InDels in the coding regions and promoter regions. The histogram shows the number of InDels, and the colored grids represent the existence of InDels in the corresponding isolates. e, f Sequence alignment of known effector genes Avr-Smira2, Avr-Smira1, Avr-amr1, and Pi22798 in TSGS and WNGZ isolates. Figure S4. Verification of RXLR effector gene expression pattern by RT-qPCR. Figure S5. Frequency of InDels in the promoter regions of P. infestans genes. The variants were called from the re-sequenced genomes of 19 isolates, and the 1 kp upstream sequence was regarded as the promoter region for each gene. a Frequency of InDels in the promoter regions of RXLR effector genes. b Frequency of InDels in the promoter regions of all genes. Figure S6. Expression and accumulation of sRNAs homologous to RXLR effector genes. a, b Ratio of effector gene with different expression levels and sRNA accumulation levels. c Number of common and regional specific RXLR effector genes between two regions. Figure S7. Verification of RXLR effector gene expression pattern by RT-qPCR. The histogram on the left shows the accumulation levels of sRNA homologous to effector genes, and the histogram on the right shows the expression levels of effector gene during infection. Figure S8. Total expression level and homologous sRNA accumulation level of RXLR effector genes. a Total abundance of homologous sRNAs in the upstream, downstream, and gene regions. b Total accumulation level of RXLR-derived sRNAs. c Total expression level of RXLR effector genes. d Proportion of effector genes that simultaneously accumulate homologous sRNAs in the coding regions and regulatory regions. Figure S9. Characteristics of homologous sRNAs accumulation of RXLR effector genes. a, d Accumulation level of sRNA homologous to sRNA-associated effectors in gene regions and promoter regions. b, e Accumulation level of sRNA homologous to reported effector genes in gene regions and promoter regions. c, f Accumulation level of sRNA homologous to Avr3a in gene region and promoter region. Statistical significance was assessed by Student’s t-test. ns, not significant. *** P &lt; 0.001.