The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

Abstract

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short‐reads, single‐molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non‐Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation‐reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

“…2015 ; Geiser et al. 2016 ; Nowak et al. 2020 ), and BAC-FISH navigated genome assembly in a duckweed genome ( S. polyrhiza ; Wang et al.…”

New model species for arctic‐alpine plant molecular ecology

“…The genomic resources published by Nowak et al (2021) include genome assembly (302 Mb assembled into eight chromosomes), gene and transposable element annotation, linkage map, and information on polymorphic sites in the genome, to mention the focal resources. It is worth noting that a chromosome level assembly is still not simple to achieve, but greatly improves understanding the evolutionary forces shaping diversity that include linked selection and unequal distribution of genomic elements across chromosomes.…”

“…It is worth noting that a chromosome level assembly is still not simple to achieve, but greatly improves understanding the evolutionary forces shaping diversity that include linked selection and unequal distribution of genomic elements across chromosomes. In Nowak et al (2021) a combination of Illumina short‐reads, Nanopore long‐reads, proximity ligation data, and linkage map from a cross between Norwegian and Alaskan strains resulted in a genome assembly of which contiguity and completeness is comparable with many Brassicaceae model species assemblies (Table 1). In particular, important steps for improving the assembly contiguity were the proximity ligation step (increased the scaffold N50 from 30 Kb to 2.9 Mb and decreased the scaffold L50 from 2663 to 30) and anchoring the scaffolds based on the linkage map (increased the scaffold N50 from 4.4 to 31 Mb).…”

“…In addition to the genomic resources, Nowak et al (2021) utilized three different approaches to investigate adaptive evolution signatures from the genome sequence of D. nivalis : (i) comparison of Pfam abundances across species, (ii) gene family composition analysis looking for significant expansions and contractions in Draba lineage, and (iii) identification of sites that have been subjects of positive selection in the branch leading to D. nivalis . These approaches were followed by gene ontology enrichment of the putatively selected loci to reveal processes, functions and cellular components specifically affected by positive selection.…”

“…Investigating the species colonization and population split history in more detail will refine the existing framework of its adaptation. Population resequencing of different groups covering different parts of its distribution range will be technically straightforward with the help of reference genome published by Nowak et al (2021). Resequencing data will allow identification of loci whose variants were favoured during the Arctic colonization, whether they are shared across the species distribution (putative preadaptation) or repeatedly adapted to similar environments independently.…”