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8 results for “P. trichocarpa”
Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)
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.
FIGURE. Orchidaceae from Honduras. A. Dichaea neglecta. B. D. panamensis. C. D. squarrosa. D. D. suaveolens. E. D. trichocarpa. F. Dichromanthus aurantiacus. G. Dinema polybulbon. H. Domingoa purpurea. I. Dryadella fuchsii. J. Elleanthus cynarocephallus. K. E. tonduzii. L. Encyclia alata. M. E. bractescens. N. E. ceratistes. O. E. chloroleuca. P. E in An Updated Checklist of the Orchidaceae of Honduras
FIGURE. Orchidaceae from Honduras. A. Dichaea neglecta. B. D. panamensis. C. D. squarrosa. D. D. suaveolens. E. D. trichocarpa. F. Dichromanthus aurantiacus. G. Dinema polybulbon. H. Domingoa purpurea. I. Dryadella fuchsii. J. Elleanthus cynarocephallus. K. E. tonduzii. L. Encyclia alata. M. E. bractescens. N. E. ceratistes. O. E. chloroleuca. P. E. cordigera. Photographs by the authors.
Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)
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Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)
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Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
Introgression can introduce novel genetic variation at a faster rate than mutation alone, and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expanded our local ancestry analysis to the whole genome of both parents to provide a comprehensive, unbiased view of introgression patterns and to identify additional candidate regions for adaptive introgression genome-wide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter-cold. The species are parapatric with extensive hybridization. Here, using local ancestry analysis, we detected asymmetric patterns of introgression across the whole genome of these two species of poplar trees adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals showed more genomic regions with unusually high levels of introgression (19 regions) compared with admixed P. balsamifera (9 regions) but also the largest introgressed peak (1.02 Mb). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles for survival and adaptation. Furthermore, we revealed overrepresentation of subtelomeric regions in P. balsamifera introgression into P. trichocarpa and possible protection of the sex-determining regions from interspecific gene flow.
Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
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Transcriptome response to embolism in stems of P. trichocarpa
GEO Series GSE32322. Populus sp.; Populus trichocarpa. 9 samples. Type: Expression profiling by array.
Screen of oligonucleotides for microarray transcriptome analysis of Populus deltoides and P. trichocarpa
GEO Series GSE12492. Populus deltoides; Populus trichocarpa x Populus deltoides; Populus trichocarpa. 12 samples. Type: Expression profiling by genome tiling array.
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