Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Abstract

Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

Tissue‐specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark

“…Conversely, tandemly duplicated genes showed depletion (Table S6). This suggests that gene expression profiles of the differentiated tissue types and possibly the tissue types themselves have evolved from gene regulatory functional diversification following the WGM events, given that WGM‐duplicated genes are enriched for transcriptional functions (for example Salojärvi et al ., ).…”

“…We further carried out enrichment analysis of the previously detected set of 913 genes under putative selective sweeps in silver birch (Salojärvi et al ., ) to explore whether these genes have a role in these tissues. All stem fractions were enriched for this set (Table S6), suggesting that local adaptation and thereby environmental conditions have a strong influence on tissue differentiation and thus wood composition in birch.…”

“…As in birch the main periderm pathways were already upregulated in F2 compared to F3, we dissected the corresponding tissues from alder to identify transcriptional differences. From the preprocessed RNA‐Seq reads, 41.65% mapped to A. glutinosa gene models (Salojärvi et al ., ; Method S3), and altogether 69% (29 436/42 653) of all gene models were expressed (Table S9).…”

Complex Haplotypes of GSTM1 Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations

“…This is not a new concept (Jin et al 2014). Such insights into the collective but varied impact of variation in a given locus have been discussed in evolutionary context in multiple species (Lin et al 2015; Salojärvi et al 2017). We are now in a position to quantitatively address this issue, especially using genealogical approaches as we described for the GSTM1 here.…”

Rapid divergence of mussel populations despite incomplete barriers to dispersal

“…Hardy-Weinberg equilibrium via ngsF (Vieira, Fumagalli, & Albrechtsen, 2013). Furthermore, we computed stairway plots (Liu & Fu, 2015) to estimate changes in effective population size (N e ) over time, using a generation time of 1 year (Morton, 1988) and a range of mutation rates from 1.0 9 10 À8 to 3.5 9 10 À8 per site per generation (Salojärvi et al, 2017).…”