Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea.
Upland Crop Breeding Research Division, Department of Southern Area Crop Science, Rural Development Administration (RDA), Miryang 50424, Republic of Korea.
Genes (Basel). 2023 Sep 30;14(10):1898. doi: 10.3390/genes14101898.
is a key component of Korean food. It contains several plant-specialized metabolites that provide medical benefits. In response to an increased interest in healthy supplement food from the public, people are focusing on the properties of Perilla. Nevertheless, unlike rice and soybeans, there are few studies based on molecular genetics on Perilla, so it is difficult to systematically study the molecular breed. The wild , 'Jeju17', was identified a decade ago on the Korean island of Jeju. Using short-reads, long-reads, and Hi-C, a chromosome-scale genome spanning 676 Mbp, with high contiguity, was assembled. Aligning the 'Jeju17' genome to the 'PC002' Chinese species revealed significant collinearity with respect to the total length. A total of 31,769 coding sequences were predicted, among which 3331 were 'Jeju17'-specific. Gene enrichment of the species-specific gene repertoire highlighted environment adaptation, fatty acid metabolism, and plant-specialized metabolite biosynthesis. Using a homology-based approach, genes involved in fatty acid and lipid triacylglycerol biosynthesis were identified. A total of 22 fatty acid desaturases were found and comprehensively characterized. Expression of the FAD genes in 'Jeju17' was examined at the seed level, and hormone signaling factors were identified. The results showed that the expression of FAD genes in 'Jeju17' at the seed level was high 25 days after flowering, and their responses of hormones and stress were mainly associated with hormone signal transduction and abiotic stress via cis-elements patterns. This study presents a chromosome-level genome assembly of 'Jeju17', the first wild to be sequenced from the Korean island of Jeju. The analyses provided can be useful in designing ALA-enhanced Perilla genotypes in the future.
紫苏是韩国食物的重要组成部分。它含有几种植物特有的代谢产物，具有药用价值。由于公众对健康补充食品的兴趣日益增加，人们开始关注紫苏的特性。然而，与大米和大豆不同，关于紫苏的分子遗传学研究很少，因此很难系统地进行分子育种研究。10 年前，在韩国济州岛发现了野生紫苏'Jeju17'。利用短读长、长读长和 Hi-C，组装了一个跨越 676 Mbp 的染色体级基因组，具有很高的连续性。将'Jeju17'基因组与中国品种'PC002'进行比对，发现总长度上存在显著的共线性。共预测了 31769 个编码序列，其中 3331 个是'Jeju17'特有的。对物种特异性基因库的基因富集分析突出了环境适应、脂肪酸代谢和植物特有的代谢产物生物合成。利用基于同源性的方法，鉴定了参与脂肪酸和脂质三酰基甘油生物合成的基因。共发现了 22 种脂肪酸去饱和酶，并进行了全面的特征描述。在种子水平上检测了'Jeju17'中 FAD 基因的表达，并鉴定了激素信号因子。结果表明，'Jeju17'中 FAD 基因在种子水平上的表达在开花后 25 天达到高峰，其对激素和胁迫的反应主要与激素信号转导和非生物胁迫有关，通过顺式元件模式。本研究提供了来自韩国济州岛的第一个被测序的野生紫苏'Jeju17'的染色体水平基因组组装。分析结果可为未来设计富含 ALA 的紫苏基因型提供有用信息。
