Gong Xun, Zhang Hantao, Guo Yinluo, Yu Shaoshuai, Tang Min
Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
School of Life Sciences, Jiangsu University, Zhenjiang, China.
Plant Genome. 2025 Mar;18(1):e20534. doi: 10.1002/tpg2.20534. Epub 2024 Nov 27.
Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.
毛叶薯蓣是一种木质藤本植物，因其富含生物活性成分，在治疗类风湿性关节炎（RA）方面具有潜在的治疗应用价值。在此，我们利用PacBio HiFi和染色质构象捕获（Hi-C）测序数据，首次完成了毛叶薯蓣核基因组的染色体水平组装。基于PacBio数据的初始组装产生了N50长度为9.71 Mb的重叠群，Hi-C数据将这些重叠群锚定到13条染色体上，总长度为273.58 Mb，与估计的基因组大小紧密匹配。包括BUSCO、长末端重复序列组装指数、转录组映射率和测序覆盖度在内的质量评估，证实了组装的高质量、完整性和连续性，鉴定出115.28 Mb的重复序列、1062个RNA基因和25270个蛋白质编码基因。此外，我们利用Illumina测序数据组装并注释了150599 bp的叶绿体基因组，其中包含121个基因，包括关键的DNA条形码，成熟酶K（matK）被证明对物种鉴定有效。系统发育分析将毛叶薯蓣定位在唇形目分支的基部，确定了显著的基因家族扩张和收缩，特别是与次生代谢物合成和DNA损伤修复相关的基因家族。代谢物分析鉴定出毛叶薯蓣中的84种活性成分，包括木犀草素的发现，预测有119个靶点可用于RA治疗，包括AKT1、Toll样受体4（TLR4）、表皮生长因子受体（EGFR）、肿瘤坏死因子（TNF）、TP53、NFKB1、janus激酶2（JAK2）、BCL2、丝裂原活化蛋白激酶1（MAPK1）和脾酪氨酸激酶（SYK）等核心靶点。突出了具有抗炎活性的黄酮类和多酚类等关键活性成分。特别是木犀草素的发现，强调了其潜在的治疗作用。这些发现为毛叶薯蓣的开发和应用提供了宝贵的基因组资源和科学依据，填补了薯蓣属和茶茱萸目在基因组方面的空白，并强调了在基因组学、转录组学和代谢组学方面进一步研究以充分挖掘其潜力的必要性。
