Additional file 1 of Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation
Creators: name: Tian, Xufang
name: Sang, Ziyang
name: Lan, Zhaohui
name: Liu, Wei
name: Feng, Ying
name: Hu, Juan
name: Chen, Faju
name: Liu, Yifei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Figure 1. Different types of Galla Chinensis. (A) Horned gall. (B) Gallnut. (C) Flower-like gall. Supplementary Figure 2. Analysis of the key phenotypic traits. Comparative analysis of gallic acid (A), fresh weight (B), gall size (C), and wall thickness (D) between wild and cultivated horned galls. The fresh weight (E), gall size (G), wall thickness (I) of the horned galls from five locations. And the fresh weight (F), gall size (H), wall thickness (J) of wild and cultivated horned galls in each location. (*, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001; ****, P &lt; 0.0001). Supplementary Figure 3. Principal Component Analysis (PCA) analysis of Bai Nianguan (BNG) (A), Bai Luzhuang (BLZ) (B), Huang Liangping (HLP) (C), and Huo Shan (HS) (D) populations based on phenotypic traits. Supplementary Figure 4. Function annotation of Rhus chinensis unigenes on the basis of public database. (A) Summary of annotations of unigenes in six databases. (B) GO classification of annotated unigenes. (C) Functional classification of unigenes based on the KEGG pathway. (D) The COG functional distribution of annotated unigenes. Supplementary Figure 5. The genetic paraments of each R. chinensis and Schlechtendalia chinensis population (WJP, BNG, BLZ, HLP, and HS represent the population from Wang Jiaping, Bai Nianguan, Bai Luzhuang, Huang Liangping, and Huo Shan, respectively.). (A). The number of alleles (N). (B) The average number of alleles (NA). (C) The effective number of alleles (NE). (D) observed heterozygosity (HO). (E) expected heterozygosity (HE). (F) Shannon’s information index (I). (G) Nei’s gene diversity index (H). (H) Polymorphism information content (PIC). Supplementary Figure 6. STRUCTURE and PCA analysis of host trees and aphids based on SSR (Simple Sequence Repeat) loci. (A) Population structure of 102 R. chinensis accessions. (B) Population structure of 102 S. chinensis accessions. (C) Population structure of R. chinensis accessions in WJP and BLZ. (D) PCA analysis of R. chinensis accessions in WJP and BLZ. (E) Population structure of R. chinensis accessions in WJP. (F) PCA analysis of R. chinensis accessions in WJP. Supplementary Figure 7. Neighbour-Joining (NJ) analysis based on the SSR loci information of R. chinensis accessions. NJ tree of individuals from BNG (A), BLZ (B), HLP (C), and HS (D). The red stars represent the wild accessions and the blue stars represent the cultivated accessions. Supplementary Figure 8. Chromatograms of negative sample (A), gallic acid standard (B), and horned gall sample (C). Supplementary Table 1. Phenotypic data among 102 horned galls. Supplementary Table 2. Correlation analysis of phenotypic traits. Supplementary Table 3. Statistic of RNA-seq, ddRAD-seq data to R. chinensis and the reference genome data of S. chinensis. Supplementary Table 4. Genetic characterization of 23 pairs of R. chinensis SSR primers and 9 pairs of S. chinensis SSR primers. Supplementary Table 5. Analysis of molecular variance (AMOVA) for R. chinensis and S. chinensis populations. Supplementary Table 6. Sampling information. Supplementary Table 7. Method validation of the high-performance liquid chromatography (HPLC) analysis in horned galls.