Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

AbstractNatural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species., Usage notesOriginal SNP data ch6 12 15_replaceSNPs in three chromosomes (6, 12, 15) for 50 reference individuals (25 pure Populus balsamifera and 25 pure P. trichocarpa) and 68 admixed individualsOriginal_data_set_ch6_12_15.zipalpha estimates in introgressed regionsData from Table 2. Alpha estimate for three introgressed P. balsamifera regions in P. trichocarpa, one in chromosome (Chr) 06 (region A) and two in chromosome 15 (B and C).alpha.zipTajima and Nucleotide Diversity estimatesData for Figure 2, Figure 4 Supporting Information (Tajimas' D) and Figure 7 Supporting Information (Nucleotide diversity).Tajima_NucleotideDiversity.zipRASPberryData for Figure 1, Figure 2 supportive information and Figure 3 supportive information.LD_HaploviewData for Figure 3 and Figure 6 supportive information.NJ analysisData from Figure 1 Supporting information and Figure 5 Supporting informationNJ.zipGene_sequencesData for Figure 4, Figure 8 supportive information and Figure 9 supportive information.971Kb_filtered_datasetThis dataset was filtered based on minimum allele frequency (MAF >0.1) and missing data (GR 0.95), for 25 reference P. trichocarpa, 25 reference P. balsamifera and 68 admixed accessions. The initial dataset consisted of 971K SNPs from 3691 genes in all 19 chromosomes.

摘要 林木自然杂交带为研究通过基因渐渗（introgression）传递适应性遗传变异提供了研究体系。此前针对关键林木树种毛果杨（Populus trichocarpa）开展的景观基因组学研究，揭示了其与姊妹物种香脂杨（Populus balsamifera）的基因混合基因组印记，并鉴定出若干本地适应候选基因。本研究利用纯合物种及野生种群渐渗个体的3条染色体基因组重测序数据，对毛果杨与香脂杨的基因渐渗模式及本地适应信号展开探究。对毛果杨渐渗个体的本地祖先分析显示，其15号染色体的端粒区域携带香脂杨祖先片段，该区域包含多个本地适应候选基因。基因组分析揭示了该区域部分基因（如PRR5、COMT1）受到选择的信号；基于基因表达变异及与适应性表型的相关性开展的功能分析表明，渐渗等位基因具有独特功能。与之形成对照的是，12号染色体上与该渐渗区域旁系同源的基因块未表现出渐渗或选择信号。我们提出假说：15号染色体上的渐渗区域为毛果杨引入了模块化（或盒式）变异。这些连锁的适应性突变与15号染色体上的基因块相关，相较于12号染色体重复区域的旁系同源基因（未表现出适应性变异信号），该基因块似乎经历了新功能化或亚功能化。香脂杨渐渗等位基因与毛果杨适应性性状表达的关联，支持了该生态重要建群物种存在适应性基因渐渗这一假说。
使用说明
1. 原始SNP数据（ch6 12 15_replaceSNPs）：涵盖50个参考个体（25个纯合香脂杨、25个纯合毛果杨）与68个渐渗个体的3条染色体（6、12、15）单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，对应压缩文件为Original_data_set_ch6_12_15.zip。
2. 渐渗区域α估计值：来自表2的数据，包含毛果杨中3个香脂杨渐渗区域的α估计值，分别位于6号染色体（区域A）与15号染色体（区域B、C），对应压缩文件为alpha.zip。
3. Tajima检验与核苷酸多样性估计值：对应图2、图4补充材料（Tajima's D）及图7补充材料（核苷酸多样性）的数据，对应压缩文件为Tajima_NucleotideDiversity.zip。
4. RASPberry数据：对应图1、图2补充材料及图3补充材料的数据。
5. LD_Haploview数据：对应图3与图6补充材料的数据。
6. 邻接（NJ）分析数据：来自图1补充材料与图5补充材料的数据，对应压缩文件为NJ.zip。
7. 基因序列数据：对应图4、图8补充材料及图9补充材料的数据。
8. 971K过滤数据集：该数据集基于最小等位基因频率（MAF>0.1）与缺失数据（基因型检出率≥0.95）进行过滤，包含25个毛果杨参考样本、25个香脂杨参考样本与68个渐渗材料。初始数据集涵盖19条染色体上3691个基因的971,000个SNP位点。