School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
Mentseekhang, Traditional Tibetan Hospital, Lhasa 850000, China.
DNA Res. 2024 Oct 1;31(5). doi: 10.1093/dnares/dsae022.
Gentiana straminea Maxim. is a perennial herb and mainly distributed in the Qinghai-Tibetan Plateau. To adapt to the extreme environment, it has developed particular morphological, physiological, and genetic structures. Also, rich in iridoids, it is one of the original plants of traditional Chinese herb 'Qinjiao'. Herein, we present its first chromosome-level genome sequence assembly and compare it with the genomes of other Gentiana species to facilitate the analysis of genomic characteristics. The assembled genome size of G. straminea was 1.25 Gb, with a contig N50 of 7.5 Mb. A total of 96.08% of the genome sequences was anchored on 13 pseudochromosomes, with a scaffold N50 of 92.70 Mb. A total of 54,310 protein-coding genes were predicted, 80.25% of which were functionally annotated. Comparative genomic analyses indicated that G. straminea experienced two whole-genome duplication events after the γ whole-genome triplication with other eudicots, and it diverged from other Gentiana species at ~3.2 Mya. A total of 142 enzyme-coding genes related to iridoid biosynthesis were identified in its genome. Additionally, we identified differences in the number and expression patterns of iridoid biosynthetic pathway genes in G. straminea compared with two other Gentiana species by integrating whole-genome sequence and transcriptomic analyses.
獐牙菜（Gentiana straminea Maxim.）是一种多年生草本植物，主要分布在青藏高原。为了适应极端环境，它形成了特殊的形态、生理和遗传结构。此外，它富含裂环烯醚萜类化合物，是传统中药“秦艽”的原始植物之一。本研究提供了獐牙菜的首个染色体水平的基因组序列组装，并与其他獐牙菜物种的基因组进行了比较，以促进基因组特征分析。獐牙菜基因组大小为 1.25 Gb，N50 为 7.5 Mb。总共 96.08%的基因组序列锚定在 13 条假染色体上，支架 N50 为 92.70 Mb。共预测到 54,310 个蛋白编码基因，其中 80.25%具有功能注释。比较基因组分析表明，獐牙菜在与其他真双子叶植物γ全基因组三倍化后经历了两次全基因组复制事件，并且在约 320 万年前与其他獐牙菜物种分化。在其基因组中总共鉴定到 142 个与裂环烯醚萜生物合成相关的酶编码基因。此外，通过整合全基因组序列和转录组分析，我们还发现了獐牙菜与其他两种獐牙菜物种在裂环烯醚萜生物合成途径基因数量和表达模式上的差异。
