Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China.
State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, China.
Mol Ecol Resour. 2020 May;20(3). doi: 10.1111/1755-0998.13142. Epub 2020 Mar 4.
Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome-level reference genome of P. euphratica (v2.0) using single-molecule sequencing and chromosome conformation capture (Hi-C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60-fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high-quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.
胡杨是一种能很好地适应极端沙漠环境的植物，是阐明树木抗非生物胁迫机制的重要模式物种。目前胡杨基因组的组装高度碎片化，存在许多缺口和错误，从而阻碍了下游应用。在这里，我们使用单分子测序和染色体构象捕获（Hi-C）技术，报道了一个改进的胡杨染色体水平参考基因组（v2.0）。与之前的参考基因组相比，我们的组装在连续性方面有了近 60 倍的提高，支架 N50 大小为 28.59 Mb。利用这个基因组，我们发现了胡杨中Gypsy 元件的广泛扩张，导致其基因组大小迅速增加，与迄今为止研究过的任何其他杨柳科物种相比都有所增加，并且可能有助于由参与胁迫耐受的基因附近的插入驱动的适应性分化。我们还在胡杨中检测到了广泛的独特结构重排，包括 2549 个易位、454 个倒位、121 个串联和 14 个片段重复。这些区域内可能有几个关键基因参与了非生物胁迫的耐受。这个高质量的基因组代表了未来杨树育种和遗传改良的宝贵资源，也为与其他杨柳科物种的比较基因组分析提供了资源。
