Interdisciplinary Program in Smart Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Genes Genomics. 2024 Dec;46(12):1387-1398. doi: 10.1007/s13258-024-01566-y. Epub 2024 Sep 25.
Oplopanax elatus is a plant of therapeutic significance in oriental medicine; however, its mass cultivation is limited owing to the difficulties in propagating it from seeds.
In this study, we investigated the transcriptome profiles and transcriptional regulatory factors expressed during plantlet regeneration from root tissues of the endangered O. elatus.
The RNA-seq results for the control and regenerated plants cultured in liquid medium for 8 weeks showed that the clean length of the control group was 11,901,667,912 and that of the 8-week sample was 10,115,155,171, indicating a clean value of 97% for both samples. The number of mapped paired-end reads was 63,922,480 for the control group and 54,146,902 for the 8-week sample. The number of genes for which at least one clean data point was mapped was 43,177 in the control group and 42,970 in the 8-week sample. The results of the differentially expressed gene analysis indicate that the number of upregulated genes in the 8-week sample was 158, and the number of downregulated genes was 424. Gene Ontology (GO) analysis of the upregulated genes revealed that GO terms were classified into 14 categories, and genes expressed in the biological process category occurred most frequently. GO terms of the downregulated genes were evenly distributed into two categories: biological process and molecular function. From the upregulated genes, eight reference genes with significant differences in expression were selected and analyzed using real-time PCR. The Oe38836 gene (late embryogenesis abundant protein M17-like isoform X1) showed the highest expression rate that was more than tenfold that of the control. Oe40610 (auxin-responsive protein SAUR21-like) and Oe07114 (glucose-1-phosphate adenyl transferase-like protein) genes showed expression levels that were increased eightfold relative to the control.
The RNA sequencing (RNA-seq) results from the plants regenerated through liquid culture of O. elatus root tissue were confirmed using real-time PCR, indicating their reliability.
奥氏独活是一种具有治疗意义的东方草药植物，但由于其种子繁殖困难，其大规模种植受到限制。
本研究调查了濒危奥氏独活根组织再生过程中的组织培养物的转录组谱和转录调控因子。
在液体培养基中培养 8 周的对照和再生植物的 RNA-seq 结果表明，对照组的清洁长度为 11901667912，8 周样本的清洁长度为 10115155171，两个样本的清洁值均为 97%。对照组的映射配对末端读数数为 63922480，8 周样本为 54146902。在对照组中，至少有一个清洁数据点映射的基因数为 43177，在 8 周样本中为 42970。差异表达基因分析的结果表明，8 周样本中上调基因的数量为 158，下调基因的数量为 424。上调基因的基因本体（GO）分析表明，GO 术语被分为 14 类，生物过程类别中表达的基因最频繁。下调基因的 GO 术语均匀分布在两个类别中：生物过程和分子功能。从上调基因中，选择了 8 个表达差异显著的参考基因进行实时 PCR 分析。Oe38836 基因（晚期胚胎丰富蛋白 M17 样同工型 X1）的表达率最高，是对照组的 10 倍以上。Oe40610（生长素响应蛋白 SAUR21 样）和 Oe07114（葡萄糖-1-磷酸腺苷转移酶样蛋白）基因的表达水平比对照组增加了 8 倍。
奥氏独活根组织通过液体培养再生的 RNA 测序（RNA-seq）结果通过实时 PCR 得到了验证，表明其可靠性。
