濒危植物山豆根全长转录组测序与不同组织比较分析

Full-length transcriptome sequencing and multi-tissue comparative analysis of the endangered plant Euchresta japonica

关键词:  山豆根, 全长转录组, 生物信息学分析, 差异表达基因, 黄酮类化合物

Key words:  Euchresta japonica, full-length transcriptome, bioinformatics analysis, differentially expressed genes(DEGs), flavonoid compounds

摘要:

山豆根(Euchresta japonica)是我国华南和西南地区特有的珍稀濒危豆科植物,其根部具有抗炎和抗癌等功能,但其基因组信息仍属空白。为此,该文通过构建其全长及比较转录组数据库,为解析其分子调控网络及活性成分合成机制提供关键数据支撑。该文采用PacBio SMRT三代测序技术,对山豆根6个组织的混合样品进行全长转录组测序,并结合Illumina平台开展不同组织转录组测序,首次建立了该物种的高质量转录组资源。结果表明:(1)获得21 703个高质量Unigenes,其中99.26%(21 543个)在七大基因功能注释数据库中获得注释。(2)鉴定到1 543个转录因子,涵盖87个家族; 挖掘到7 649个SSR位点,分布于6 263个Unigenes中,以混合微卫星和三碱基重复类型为主。(3)多组织比较转录组分析发现16 220个非冗余差异表达基因(DEGs),果实与花序、侧根与果实间差异最显著,花序、果实和侧根中存在大量高表达基因。(4)超过半数的黄酮类化合物合成相关基因在侧根和/或花序中高表达,与代谢物积累模式一致,表明侧根和花序是黄酮类化合物生物合成的关键场所。该研究填补了山豆根属转录组信息的空白,为解析其药用活性成分的生物合成途径、挖掘关键功能基因及开发分子标记提供了重要遗传资源。

Abstract:

Euchresta japonica is a rare and endangered legume species endemic to southern and southwestern China, valued for the anti-inflammatory and anti-cancer properties of its roots. Nevertheless, genomic information for this species remains largely unavailable. To address this gap, we constructed a full-length and comparative transcriptome database to provide key molecular insights into its regulatory networks and the biosynthesis of bioactive compounds. Using PacBio SMRT third-generation sequencing technology, we performed full-length transcriptome sequencing on a mixed sample from six tissues of E. japonica, combined with Illumina platform for various transcriptome profiling, thereby establishing the first high-quality transcriptomic resource for this species. The results were as follows:(1)A total of 21 703 high-quality Unigenes were obtained, of which 99.26%(21 543)were annotated in seven major gene functional databases.(2)A total of 1 543 transcription factors spanning 87 families were identified, and 7 649 SSR loci were detected distributed across 6 263 Unigenes, with compound SSR and tri-nucleotide repeats being the most abundant.(3)Comparative transcriptomic analysis across six tissues revealed 16 220 non-redundant differentially expressed genes(DEGs). The most pronounced differences were observed between fruit and inflorescence, and between lateral root and fruit, with substantial numbers of highly expressed genes detected in inflorescence, fruit, and lateral root.(4)Over half of the flavonoid biosynthesis-related genes were highly expressed in lateral root and/or inflorescence, consistent with metabolite accumulation patterns, indicating these tissues are key sites for flavonoid biosynthesis. This study provides the first comprehensive transcriptome resource for the genus Euchresta, offering valuable genetic data for elucidating the biosynthetic pathways of bioactive compounds, identifying key functional genes, and developing molecular markers.