Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood) Suarez-Gonzalez, Adriana; Hefer, Charles; Christie, Camille; Corea, Oliver; Lexer, Christian; Cronk, Quentin C. B.; Douglas, Carl J.; Hefer, Charles A.; Christe, Camille
Natural 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 notes
Original 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.