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Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)
Geraldes, Armando; Hefer, Charles A.; Capron, Arnaud; Kolosova, Natalia; Martinez-Nuñez, Felix; Soolanayakanahally, Raju Y.; Stanton, Brian; Guy, Robert D.; Mansfield, Shawn D.; Douglas, Carl J.; Cronk, Quentin C. B. — 2015-02-26 All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of ‘turnover’ of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
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Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
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Suarez-Gonzalez, Adriana; Hefer, Charles A.; Lexer, Christian; Cronk, Quentin C.B.; Douglas, Carl J.; Cronk, Quentin C. B. — 2018-02-26 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.
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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)
Huang, Daisie I.; Hefer, Charles A.; Kolosova, Natalia; Douglas, Carl J.; Cronk, Quentin C. B. — 2015-05-18 As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now-extinct North American poplar.

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(Author: Hefer, Charles A.)

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