An Improved Chromosome-scale Genome Assembly and Population Genetics resource for<i>Populus tremula</i>

Schiffthaler, Bastian; Robinson, Kathryn M.; Lü, Hui; Bernhardsson, Carolina; Westman, Sara; Rendon, Martha; Delhomme, Nicolas; Jenkins, Jerry; Wang, Jing; Mähler, Niklas; Richau, Kerstin H.; Albrectsen, Benedicte Riber; Park, Eung‐Jun; Schmutz, Jeremy; Jansson, Stefan; Ingvarsson, Pär K.; Street, Nathaniel R.

doi:10.1101/805614

Cited by 19 publications

(24 citation statements)

References 182 publications

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“…S1 and Table S1). The leaves were dried in silica gel first and were then used All raw sequencing reads were mapped to the P. tremula 2.0 reference genome (Schiffthaler, et al 2019) using BWA-MEM, as implemented in bwa v0.7.10 (Li 2013).…”

Section: Sampling Sequencing and Read Processingmentioning

confidence: 99%

“…Among all woody perennial angiosperm species, the genome of P. trichocarpa was sequenced and published first (Tuskan, et al 2006). In addition to Populus trichocarpa , another well-annotated genome assembly is available ( P. tremula ; Schiffthaler, et al 2019). Taken together, the rich genomic resources, small genomes and widespread geographic distribution make the Populus system a useful model to address open questions regarding the formation of genomic islands along the speciation continuum.…”

Section: Introductionmentioning

confidence: 99%

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Drivers of genomic landscapes of differentiation acrossPopulusdivergence gradient

Shang

Rendón-Anaya

Paun

et al. 2021

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Investigating genome-wide variation patterns along a speciation continuum is of central importance to understand the evolutionary processes contributing to lineage diversification. To identify which forces have shaped the genomic landscapes in Populus, we resequenced 201 whole-genomes from eight closely related species, with pairs of species at different stages along the speciation continuum. Using population structure and identity by descent analyses, we show extensive introgression between some species pairs, especially those with parapatric distributions. Inference of historical changes in effective population sizes support species-specific demographic trajectories, including recent population expansions in species characterized by broad present-day distributions. We observe highly conserved genomic landscapes, either focusing on within-species (genetic diversity: π and recombination rate: ρ) or among-species variation (relative divergence: FST and absolute divergence: DXY ). Independent of the stage across the divergence continuum, we recovered positive correlations between the pair π and ρ and the pair DXY and ρ across all species pairs, which is consistent with a substantial contribution of linked selection in shaping these genomic landscapes. However, the positive correlations between π and DXY became weaker as the overall divergence level (da) increased, suggesting that background selection is not the only factor at play. Positive correlations between FST and DXY in all species pairs, regardless of the rate of gene flow, also indicates the high FST could be due to divergent sorting of ancient polymorphism before speciation. Our study showcases the importance of investigating genomic patterns on multiple species across the speciation continuum to better understand the genomic landscapes of diversity and differentiation.

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Section: Sampling Sequencing and Read Processingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Drivers of genomic landscapes of differentiation acrossPopulusdivergence gradient

Shang

Rendón-Anaya

Paun

et al. 2021

Preprint

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“…Our collection comprises 411 P. tremula individuals sampled from China [39], Russia, Latvia, Norway, Sweden, Iceland and Scotland (Figure 1A; Additional File2: Table S1). Sequencing reads for all individuals were mapped against the reference P. tremula v2.0 genome [18] and obtained ∼20.8e 6 SNPs after several filtering steps (depth of coverage, missingness, level of heterozygosity and batch effect caused by the incorporation of samples in the Swedish collection from two different sequencing platforms; Additional File1: Figure S1,2). It should be highlighted that the removal of false heterozygous positions did not alter the results of the downstream analyses (Additional File1: Figure S5).…”

Section: Resultsmentioning

confidence: 99%

“…Re-sequenced accessions were mapped against the reference genome of P. tremula v2.0 [18], using BWA (v0.7.17; [19] – mem alignments for paired-end reads using default parameters. Post-mapping filtering removed reads with MQ<20 (using samtools v1.10; [20].…”

Section: Methodsmentioning

confidence: 99%

Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremulaL.)

Rendón-Anaya

Wilson

Sveinsson

et al. 2021

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Understanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ~500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

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“…And from NGDC's GSA (Bioproject PRJACA002485 -accessions CRR176864 to CRR176875 and CRR176894 to CRR176905) for P. alba (Yang et al, 2021). Reads were trimmed using Trimmomatic (Bolger et al, 2014) with the following parameters: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAI-LING:3 SLIDINGWINDOW:4:15 MINLEN:36, and subsequently mapped to the reference genome of female P. tremula (Schiffthaler et al, 2019), with bowtie2 (Langmead and Salzberg, 2012) using default parameters. Read coverage was visualized for the previously described sex-linked region using R ("R Core Team, " 2018) with the packages Rsamtools (Morgan et al, 2021), GenomicRanges (Lawrence et al, 2013), zoo (Zeileis and Grothendieck, 2005), ggplot2 (Wickham, 2016) and tidyverse (Wickham et al, 2019).…”

Section: Re-sequencing Data Analysismentioning

confidence: 99%

The genetic basis of sex determination in Populus provides molecular markers across the genus and indicates convergent evolution

et al. 2021

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Many dioecious angiosperms are trees, which only flower after years of vegetative development and do not usually exhibit marked secondary sexual dimorphism. Nevertheless, if the genetic basis of sex determination is known, the sex of an individual can be determined using molecular markers. Here, we report that in the genus Populus sect. Populus an XY system of sex determination, which is found in P. tremula and P. tremuloides, likely re-evolved from a ZW system present in P. alba, P. adenopoda and P. qiongdaoensis. Strikingly, this new XY system is mechanistically identical to the older system found in several species of the Populus sections Tacamahaca, Aigeiros and Turanga demonstrating a remarkable example of convergent evolution. In both XY systems, male-specific inversely repeated sequences appear to silence the ARR17 gene, which functions as a sex switch, via small interfering RNAs and DNA methylation. In the ZW system, female-specific copies of ARR17 appear to regulate dioecy. With this detailed information on the genetic basis of sex determination it was possible to develop molecular markers that can be utilized to determine the sex in seedlings and non-flowering trees of different poplar species. We used the female-specific ARR17 gene to develop a sex marker for P. alba and P. adenopoda. For P. grandidentata, we employed the male-specific ARR17 inverted repeat. Finally, we summarize previously described markers for P. tremula, P. tremuloides, P. trichocarpa, P. deltoides and P. nigra. These markers can be useful for poplar ecologists, geneticists and breeders.

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An Improved Chromosome-scale Genome Assembly and Population Genetics resource forPopulus tremula

Cited by 19 publications

References 182 publications

Drivers of genomic landscapes of differentiation acrossPopulusdivergence gradient

Drivers of genomic landscapes of differentiation acrossPopulusdivergence gradient

Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremulaL.)

The genetic basis of sex determination in Populus provides molecular markers across the genus and indicates convergent evolution

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