Liu Jie-Xia, Jiang Qian, Tao Jian-Ping, Feng Kai, Li Tong, Duan Ao-Qi, Wang Hao, Xu Zhi-Sheng, Liu Hui, Xiong Ai-Sheng
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, 210095, Nanjing, China.
Hortic Res. 2021 Dec 1;8(1):262. doi: 10.1038/s41438-021-00707-8.
Water dropwort (Liyang Baiqin, Oenanthe javanica (BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing of O. javanica via HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research on O. javanica (database homepage: http://apiaceae.njau.edu.cn/waterdropwortdb ). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship between O. javanica and Daucus carota was the closest. Twenty-five gene families of O. javanica were found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation in O. javanica under different water conditions were further investigated. Two miRNA and target gene pairs (miR408 and Oja15472, miR171 and Oja47040) were remarkably regulated by water stress. The obtained reference genome of O. javanica provides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of the O. javanica response to water stress, including morphological, anatomical, and genetic differentiation.
水芹（溧阳白芹，Oenanthe javanica (BI.) DC.）是一种来自伞形科的多年生水生植物，富含蛋白质、膳食纤维、维生素和矿物质。它通常生长在湿润的土壤中，甚至可以在水中生长。本文首次报道了通过HiSeq 2000测序技术对水芹进行全基因组测序。其基因组大小为1.28 Gb，包含42270个基因，其中93.92%的基因可进行功能注释。建立了水芹全基因组序列在线数据库Water dropwortDB，以分享研究结果并促进对水芹的进一步研究（数据库主页：http://apiaceae.njau.edu.cn/waterdropwortdb ）。Water dropwortDB提供全基因组和转录组序列以及一个基本局部比对搜索工具。与其他物种的比较分析表明，水芹与胡萝卜的进化关系最为密切。发现水芹有25个基因家族发生了扩张，并进一步研究了与水芹在不同水分条件下表型和解剖学分化相关的一些遗传因素（如基因和miRNA）。两个miRNA与靶基因对（miR408和Oja15472、miR171和Oja47040）受水分胁迫的显著调控。获得的水芹参考基因组为未来的研究工作提供了重要信息，从而使深入的遗传育种和基因编辑成为可能。本研究也为理解水芹对水分胁迫的响应，包括形态、解剖和遗传分化，提供了基础。
