The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.黄瓜（Cucumis sativus L.）是广泛栽培的作物，起源于东喜马拉雅山脉，其次生驯化区域涵盖温带、亚热带等气候差异极大的生境。本研究旨在解析不同栽培黄瓜品种间的适应性基因组差异，以及调控植物对不同生态系统的遗传适应性与生物多样性的进化分子机制。本研究报道了欧洲北部Borszczagowski品种（品系B10）的黄瓜基因组草图序列，并与已发表的其他黄瓜基因组（中国品种‘中国长’，品系9930）、拟南芥（Arabidopsis thaliana）、毛果杨（Populus trichocarpa）以及水稻（Oryza sativa）开展了比较基因组学分析。黄瓜基因组存在广泛的染色体重排，特定基因（如参与光合作用、呼吸作用、糖代谢、叶绿素降解、基因表达调控、光氧化胁迫耐受、非最适温度耐受及铵离子同化的基因）的数量存在显著差异，同时同源基因家族启动子区域内脱落酸（abscisic acid）、脱水响应与乙烯响应顺式调控元件（cis-regulatory elements, CREs）的分布模式亦存在明显区别，上述差异共同造就了黄瓜特异性的适应特征。对未驯化的拟南芥与黄瓜幼苗施加脱落酸处理后，拟南芥可诱导出中等耐寒性，但黄瓜并未出现该表型，结合脱落酸特异性顺式调控元件的分布分析，该实验结果揭示了黄瓜比拟南芥对中等冻胁迫更为敏感的潜在原因。对上述五个基因组的比较分析显示，每个物种及/或品种的同源基因启动子区域内，顺式调控元件含量均存在特异性谱图。本研究结果为植物环境适应性的基础与应用研究提供了极具价值的原创性资源，有望助力培育在异质环境中生长性能更优、产量更高的新型作物。