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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 A. ; Christe, Camille ; Corea, Oliver ; Lexer, Christian ; Cronk, Quentin C. B. ; Douglas, Carl J.

Molecular ecology, 2016-06, Vol.25 (11), p.2427-2442 [Periódico revisado por pares]

England: John Wiley & Sons, Ltd

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  • Título:
    Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)
  • Autor: Suarez-Gonzalez, Adriana ; Hefer, Charles A. ; Christe, Camille ; Corea, Oliver ; Lexer, Christian ; Cronk, Quentin C. B. ; Douglas, Carl J.
  • Assuntos: Adaptation ; Adaptation, Biological - genetics ; adaptive introgression ; admixture ; Alleles ; Botany ; Chromosome Mapping ; Chromosomes, Plant - genetics ; DNA, Plant - genetics ; Genome, Plant ; Genomics ; Haplotypes ; Hybridization ; Hybridization, Genetic ; local adaptation ; Phenotype ; Polymorphism, Single Nucleotide ; Populus ; Populus - classification ; Populus - genetics ; Populus balsamifera ; Populus trichocarpa ; Selection, Genetic ; Sequence Analysis, DNA ; Telomere - genetics
  • É parte de: Molecular ecology, 2016-06, Vol.25 (11), p.2427-2442
  • Notas: http://dx.doi.org/10.1111/mec.13539
    ThinkSwiss Fellowship
    Fig. S1 Neighbor-Joining (NJ) trees of 25 pure P. balsamifera, 25 pure P. trichocarpa, and 146 additional P. trichocarpa individuals from phased SNPs of an introgressed region of chromosome 15. Fig. S2 Proportion of P. balsamifera ancestry in admixed P. trichocarpa individuals analyzed in three sliding window sizes. Fig. S3 Proportion of P. trichocarpa ancestry in admixed P. balsamifera individuals across chromosomes 6, 12, and 15. Fig. S4 Neighbor-Joining (NJ) tree of parental linages based on the first 880 kb of chromosome 15. Fig. S5 Tajima's D analysis in pure P. balsamifera and P. trichocarpa individuals in chromosome 6 and 12 based on 50-kb windows. Fig. S6 Linkage disequilibrium (LD) decay with distance. Fig. S7 Nucleotide diversity (π) levels across the first 1 MB of chromosome 15. Fig. S8 Partial protein alignment of different COMT1 homologs. Fig. S9 TTG1 and PRR5 alleles and geographic distribution of haplotypes in P. trichocarpa populations. Fig. S10 Relative gene expression (based on 2-ΔCT) of COMT1 among P. trichocarpa individuals with different COMT1 alleles. Fig. S11 Box plot of the mean-centered FPKM values for the expression of the top 25 genes co-expressed with PRR5 in xylem. Fig. S12 LD plot of COMT1 in individuals from northern and central parts of P. trichocarpa's range. Fig. S13 Three-dimensional protein model of P. trichocarpa COMT1 based on template 1KYW.Table S1. List of P. trichocarpa and P. balsamifera accessions used in this study and biogeographical data (latitude, longitude, elevation). Table S2 Parameters for the raspberry model with the highest log likelihood value, based on a whole genome SNP data set (see supplementary M&M) in 25 pure P. balsamifera, 25 pure P. trichocarpa and 68 admixed individuals. Table S3 Candidate genes for local adaptation across P. trichocarpa's range, in chromosome 6 and 15 based on FST outlier tests and/or association analysis with environmental variables and phenotypic traits (Geraldes et al. 2014; McKnown et al. 2014), and using a 34 k SNP chip. Table S4 Quantitive reverse transcription PCR (qTt-PCR) to test the levels of expression of COMT1 genes in different P. trichocarpa genotypes. Table S5 List of genes in introgressed region from chromosome 6 and 15 based on local ancestry analysis in raspberry. Table S6 A Introgressed genes from P. balsamifera in P. trichocarpa in a telomeric region of chromosome 15, corresponding Arabidopsis ortholog gene code, GO term or protein group enriched in the introgressed regions, Tajima's D values higher than 99% of the distribution, genes with significant positive values of alpha and nucleotide diversity values higher than 95% of the distribution in P. balsamifera. Table S7 List of genes in introgressed region B in chromosome 15 that showed significantly different levels of expression in admixed (bb, bt) individuals compared to pure P. trichocarpa individuals. Table S8 A Genes from the first introgressed region of chromosome 15 that showed associations with traits related to phenology, ecophysiology and biomass (McKown et at. 2014).Appendix S1 Materials & methods.
    Natural Sciences and Engineering Research Council of Canada Discovery - No. RGPIN 36485-12
    Genome Canada Large-Scale Applied Research Program - No. 168BIO
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    Swiss National Science Foundation (SNF)
    istex:7199967569FE0587973AB54F9767DC860D024BDD
    Biodiversity Research Integrative Training & Education (BRITE) program
    ArticleID:MEC13539
    ObjectType-Article-1
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  • Descrição: 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 Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the 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 subfunctionalization 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.
  • Editor: England: John Wiley & Sons, Ltd
  • Idioma: Inglês
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