Jiang Lan, Lin Mengfei, Wang Han, Song Hui, Zhang Lin, Huang Qingyu, Chen Renrui, Song Cheng, Li Guohui, Cao Yunpeng
Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, 241000, China.
Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330224, Jiangxi, China.
Plant J. 2022 Sep;111(5):1340-1353. doi: 10.1111/tpj.15892. Epub 2022 Jul 29.
Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.
白及，俗称白芨，是一种用于传统中药的植物；它因其药用价值而备受推崇，因此具有很高的经济价值。在此，我们报道了白及的高质量单倍型解析基因组，单倍型A（23.7亿碱基对，支架N50为1.4639亿碱基对，重叠群N50为165万碱基对）和单倍型B（24.3亿碱基对，支架N50为1.5022亿碱基对，重叠群N50为166万碱基对），它们由高保真（HiFi） reads和染色体构象捕获（Hi-C） reads组装而成。我们发现证据表明白及经历了两次全基因组复制（WGD）事件：一次是大多数单子叶植物共有的古老WGD事件，另一次是所有兰花特有的近期WGD事件。我们还重建了18条古老染色体的祖先兰花核型（AOK）和16条现代白及染色体的进化轨迹。比较基因组分析表明，白及中扩增的基因家族可能在次生代谢物生物合成和环境适应中发挥重要作用。通过整合基因组和转录组数据，我们从九个基因家族中鉴定出10个核心成员，它们可能参与白及多糖（BSP）的生物合成。基于病毒诱导基因沉默（VIGS）和酵母双杂交实验，我们提出了一个MYB转录因子（TF），即BsMYB2，它可以通过直接与八个与BSP相关的关键基因相互作用来调节BSP的生物合成：sacA1、HK1、scrK1、scrK2、GPI1、manA1、GMPP1和UGP2_1。我们的研究将增进对兰花进化的理解，并加速白及的分子辅助育种，以改善其药用价值性状。
