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Additional file 2 of Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens

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posted on 2022-08-25, 07:11 authored by Zhudong Liu, Longsheng Xing, Wanlong Huang, Bo Liu, Fanghao Wan, Kenneth F. Raffa, Richard W. Hofstetter, Wanqiang Qian, Jianghua Sun
Additional file 2: Figure S1. Genome survey result based on k-mer frequency analysis. K-mer frequency analysis was performed using Jellyfish (k-mer = 17) based on Illumina paired-end sequencing reads of genomic DNA. Genome size, repeat sequence content, and heterozygosity ratio were estimated based on k-mer frequency distribution using GenomeScope 2.0. The estimated genome size was 372.97 Mb. Figure S2. Linkage group contact map informed by Hi-C sequencing data in the red turpentine beetle genome. Fourteen linkage groups were generated after the clustering of contact map. The color bar indicates the frequency of Hi-C interaction intensity from low (yellow) to high (red) in the plot. Figure S3. Venn diagram showing the common and unique gene families across four Coleoptera species. Gene families were assigned by TreeFam database in four Coleoptera species, the red turpentine beetle Dendroctonus valens, the mountain pine beetle Dendroctonus ponderosae, the red flour beetle Tribolium castaneum, and the Asian long-horned beetle Anoplophora glabripennis. Figure S4. Synteny analysis between Dendroctonus valens and two closely related species. Dot plot representation of the syntenic relationship between D. valens and the species in the same genus, Dendroctonus ponderosae. Notably, D. valens linkage groups (LGs) showed strong syntenic relationship with D. ponderosae pseudo-chromosomes. Additionally, many fission and fusion events were observed between D. valens and D. ponderosae. (b) Genome-wide synteny relationship between D. valens and two Coleoptera insects, D. ponderosae and Tribolium castaneum. As shown in the figure, Dpochr1 was formed by the fusion of four complete LGs in D. valens (i.e. LG1, LG4, LG10, and LG11). By contrast, Dpochr9 fused with Dpochr12 to generate LG13 of D. valens. Genome-wide synteny analysis was performed using the MCScan pipeline of JCVI utility libraries. Figure S5. Global representation of sampling sites of different geographical populations and RTB movement. The putative invasion and spread routes was also indicated in the map based on data collected from literature (The green dot denotes the area Canada where RTB originates. The orange solid arrows indicate the west route of RTB spread in North America, and the blue solid arrows show the east route of RTB spread in North America. The red dotted arrow represents the putative invasion route from the west coast of North America to Shanxi province of China). Resequencing samples were collected from six states (red dots) in the original country North America (including Arizona [AZ], Colorado [CO], California [CA], Montana [MT], Wisconsin [WI], and Minnesota [MN]) and five provinces (blue dots ) in the invaded country China (including Liaoning [LN], Inner Mongolia [NM], Hebei [HB], Shanxi [SX], and Shaanxi [SHX]). Figure S6. Number of genomic regions showing signals of selective sweep. Selective sweep analysis was conducted based on genetic differentiation index (FST) and nucleotide diversity (Pi) ratio in three contrast groups, including AZCO vs. CHN (a), CAMT vs. CHN (b), and WIMN vs. CHN (c). The left panel represents the selection status in North American subpopulations, and the right panel stands for the selection status in China populations. The genomic regions that were under selection were determined by the intersection set of FST outliers (top 5% quantile) and Pi ratio outliers (top 5% quantile), which corresponds to the overlapping part in the Venn diagram.

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National Key Research and Development Program of China National Natural Science Foundation of China Science, Technology and Innovation Commission of Shenzhen Municipality

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