西藏沙棘染色体水平基因组组装揭示了高海拔适应和类黄酮生物合成的机制

Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis

Abstract

Background

As an endemic shrub of the Qinghai-Tibetan Plateau (QTP), the distribution of Hippophae tibetana Schlecht. ranges between 2800 and 5200 m above sea level. As the most basal branch of the Hippophae genus, H. tibetana has an extensive evolutionary history. The H. tibetana is a valuable tree for studying the ecological evolution of species under extreme conditions.

Results

Here, we generated a high-quality chromosome-level genome of H. tibetana. The total size of the assembly genome is 917 Mb. The phylogenomic analysis of 1064 single-copy genes showed a divergence between 3.4 and 12.8 Mya for H. tibetana. Multiple gene families associated with DNA repair and disease resistance were significantly expanded in H. tibetana. We also identified many genes related to DNA repair with signs of positive selection. These results showed expansion and positive selection likely play important roles in H. tibetana’s adaptation to comprehensive extreme environments in the QTP. A comprehensive genomic and transcriptomic analysis identified 49 genes involved in the flavonoid biosynthesis pathway in H. tibetana. We generated transgenic sea buckthorn hairy root producing high levels of flavonoid.

Conclusions

Taken together, this H. tibetana high-quality genome provides insights into the plant adaptation mechanisms of plant under extreme environments and lay foundation for the functional genomic research and molecular breeding of H. tibetana.

**摘要**

**背景**  
作为青藏高原（QTP）的特有灌木，西藏沙棘（Hippophae tibetana Schlecht.）的分布范围在海拔2800米至5200米之间。作为沙棘属（Hippophae）中最原始的分支，西藏沙棘有着悠久的进化历史。它是一种研究植物在极端条件下生态进化的宝贵物种。

**结果**  
在此，我们生成了西藏沙棘的高质量染色体水平基因组。组装基因组的总大小为917 Mb。对1064个单拷贝基因的系统发育基因组分析显示，西藏沙棘的分化时间在340万至1280万年前之间。与DNA修复和抗病性相关的多个基因家族在西藏沙棘中显著扩张。我们还鉴定出许多与DNA修复相关的基因表现出正选择的迹象。这些结果表明，扩张和正选择可能在西藏沙棘适应青藏高原极端环境方面发挥了重要作用。通过全面的基因组和转录组分析，我们鉴定出49个参与黄酮类生物合成途径的基因。我们还培育出了能够产生高水平黄酮类物质的转基因沙棘毛状根。

**结论**  
综上所述，西藏沙棘的高质量基因组为研究植物在极端环境下的适应机制提供了见解，并为西藏沙棘的功能基因组研究和分子育种奠定了基础。

Background

Known as the Himalaya Plateau, the Qinghai-Tibet Plateau (QTP) is the world’s largest and highest plateau [1]. In the QTP, considerable geological uplifts have occurred seven times since the Pliocene [2]. For example, it has been estimated that the QTP mountains were uplifted three times between 0.6 and 1.3 million years ago (Mya) [3]. Increasing altitude has resulted in extensive glaciation on the QTP. Naynayxungla Glaciation, the largest glaciation in the QTP, began approximately 1.2 Mya and peaked between 0.6 and 0.8 Mya. The uplift of the Qinghai-Tibet Plateau (QTP) has led to significant climatic and environmental transformations in the plateau region. Low temperature, low oxygen, reduced pathogen incidence, and strong UV radiation now characterize the QTP conditions, creating an ideal environment for studying adaptive evolution [4, 5]. The diversifications of many endemic species are highly consistent with environmental changes and climate change [6]. A majority of genome-wide studies on adaptive evolution have been conducted on vertebrates and humans [7,8,9]. According to these studies, genes involved in hypoxia responses, energy metabolism, and skeletal development are undergoing positive selection and rapid evolution. Recently, a few studies have been conducted on wild plants in this region using whole-genome analysis to study adaptive evolution, including Tibetan hulless barley [10], wild barley [11], maca [12], and Eutrema [13].

**背景**  
青藏高原（QTP），也被称为喜马拉雅高原，是世界上最大和最高的高原 [1]。自上新世以来，青藏高原经历了七次显著的地质抬升 [2]。例如，据估计，青藏高原的山脉在距今约60万至130万年前之间发生了三次抬升 [3]。海拔的不断升高导致青藏高原上广泛发育冰川。纳木错冰期是青藏高原最大的冰期，大约始于120万年前，并在60万至80万年前达到顶峰。青藏高原的抬升导致了该地区显著的气候和环境变化 [4, 5]。如今，低温、低氧、病原体发病率降低以及强紫外线辐射成为青藏高原的典型环境特征，这为研究适应性进化提供了一个理想的环境。许多特有物种的多样化与环境变化和气候变化高度一致 [6]。目前，大多数关于适应性进化的全基因组研究主要集中在脊椎动物和人类 [7, 8, 9]。根据这些研究，参与低氧反应、能量代谢和骨骼发育的基因正在经历正选择和快速进化。最近，一些研究开始利用全基因组分析研究该地区的野生植物的适应性进化，包括西藏裸大麦 [10]、野生大麦 [11]、蔓菁 [12] 和盐芥 [13]。

Flavonoids from sea buckthorn (H. rhamnoides L.) were used to prevent and manage chronic diseases such as diabetes, cardiovascular disease, and cancer [17]. Sea buckthorn leaves, roots, stems, and fruits have high total concentration [18]. As a subgroup of flavonoids, flavonols are the most abundant in sea buckthorn. In sea buckthorn leaves and berries, the isorhamnetin glycosides are typically the most significant flavonols [19]. A variety of genetic and environmental factors influence flavonoid accumulation in sea buckthorn [18]. There are lots of genes involved in the flavonoid biosynthesis pathways, including phe