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

AbstractThe Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first complete 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., Usage notesPlease see ReadMe.txt for a full description of each file.摘要 北极是地球上最为极端的陆地环境之一。本研究首次报道了适配高北极环境的植物雪葶苈（Draba nivalis，十字花科 Brassicaceae）的完整基因组组装结果，该物种是探究植物适应极端严酷环境胁迫的优质模式物种。本研究采用迭代支架组装（iterative scaffolding）策略，整合短读长测序数据（short-reads）、单分子长读长测序数据（single-molecule long reads）、邻近连接测序数据（proximity ligation）以及遗传图谱信息，最终获得302 Mb的基因组组装结果，该组装具有极高连续性，其中91.6%的序列被锚定至8条染色体（该类群的基础染色体数）。为筛选出可能助力该物种适应北极环境胁迫的候选基因与基因家族，本研究选取9种非北极十字花科物种开展比较基因组学分析。结果显示，雪葶苈基因组中与干旱、低温胁迫相关的基因家族发生显著扩张，涉及氧化还原稳态维持、减数分裂及信号通路等功能相关基因家族。上述功能相关基因家族的扩张，部分由转座因子（transposable element）的活性所介导。正选择检验筛选出一批与减数分裂、光周期响应，以及低温、干旱和氧化应激响应相关的候选基因。本研究结果揭示了雪葶苈基因组中多维度的胁迫适应格局，为该物种作为北极模式植物的后续研究提供了重要方向。 使用说明 各文件的完整说明请参阅ReadMe.txt文档。