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黄育通,邢艳萍,门文效,黄彦昌,杨燕云,康廷国,窦德强,许亮.药用植物粗茎鳞毛蕨转录组测序分析[J].广西科学,2025,32(5):964-975. [点击复制]
- HUANG Yutong,XING Yanping,MEN Wenxiao,HUANG Yanchang,YANG Yanyun,KANG Tingguo,DOU Deqiang,XU Liang.Transcriptome Sequencing Analysis of the Medicinal Plant Dryopteris crassirhizoma[J].Guangxi Sciences,2025,32(5):964-975. [点击复制]
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| 药用植物粗茎鳞毛蕨转录组测序分析 |
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黄育通1, 邢艳萍1, 门文效1, 黄彦昌1, 杨燕云1, 康廷国1, 窦德强1,2, 许亮1,2
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| (1.辽宁中医药大学药学院, 辽宁大连 116600;2.辽宁省中药质量及资源开发专业技术创新中心, 辽宁沈阳 110847) |
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| 摘要: |
| 为获取粗茎鳞毛蕨(Dryopteris crassirhizoma)的转录组信息并分析其基因表达特征，本研究采用Illumina HiSeqTM 2000 150PE高通量测序平台,对其叶、叶柄、叶轴、根和根状茎进行转录组测序分析。结果表明：经Trinity拼接并去冗余后，共获得147 690个unigenes，在核酸序列库(Nucleotide sequence database，NT)、非冗余蛋白质数据库(Non-Redundant protein database，NR)、Swiss-Prot 蛋白质序列数据库(Swiss-Prot protein sequence database，Swiss-Prot)、京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes，KEGG)、直系同源蛋白质群数据库(Clusters of Orthologous Groups of proteins，COG)和基因本体库(Gene Ontology，GO)中获得注释的unigenes数量分别为91 758、57 578、60 535、56 670、41 446、63 027个。GO分类注释得到3大类56个分支，KEGG代谢通路注释到129条标准通路，其中23条为次生代谢通路。蛋白质编码框序列94 731个，以短序列为主。简单重复序列(Simple Sequence Repeat，SSR)分析发现28 079个SSRs，以二核苷酸SSRs最多，占总SSRs数量的70.12%。单核苷酸多态性(Single Nucleotide Polymorphism，SNP)分析检测到叶、叶柄、叶轴、根和根状茎的SNP数量分别为23 139、21 246、28 280、55 409、17 084个。叶柄与根状茎差异基因表达量分析显示上调基因13 829个、下调基因24 250个。GO功能富集分析结果表明，在叶柄和根状茎组织中共富集到226个与苯丙烷类代谢途径相关的差异表达基因。本研究结果可为后续深入探究粗茎鳞毛蕨次生代谢通路、间苯三酚类与黄酮类等物质的生物合成及基因功能提供转录组数据支持。 |
| 关键词: 粗茎鳞毛蕨 转录组 功能注释 代谢通路 差异基因 |
| DOI：10.13656/j.cnki.gxkx.20251208.010 |
| 投稿时间：2025-06-23修订日期：2025-08-07 |
| 基金项目:辽宁省“百千万人才工程”项目(2021921039)，中央本级重大增减支项目“名贵中药资源可持续利用能力建设项目”(2060302)和辽宁省教育厅项目(JYTMS20231834)资助。 |
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| Transcriptome Sequencing Analysis of the Medicinal Plant Dryopteris crassirhizoma |
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HUANG Yutong1, XING Yanping1, MEN Wenxiao1, HUANG Yanchang1, YANG Yanyun1, KANG Tingguo1, DOU Deqiang1,2, XU Liang1,2
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| (1.School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Liaoning, 116600, China;2.Liaoning Province Technical Innovation Center for Traditional Chinese Medicine Quality and Resource Development, Shenyang, Liaoning, 110847, China) |
| Abstract: |
| To obtain transcriptomic information of Dryopteris crassirhizoma and analyze its gene expression characteristics,this study performed transcriptome sequencing on leaves,petioles,leaf axes,roots,and rhizomes by using the Illumina HiSeqTM 2000 150PE high-throughput sequencing platform.The results showed that after assembly with Trinity and removal of redundancy,a total of 147 690 unigenes were obtained.Annotation was performed against the Nucleotide sequence database (NT),Non-Redundant protein database (NR),Swiss-Prot protein sequence database (Swiss-Prot),Kyoto Encyclopedia of Genes and Genomes (KEGG),Clusters of Orthologous Groups of proteins (COG),and Gene Ontology (GO),with 91 758,57 578,60 535,56 670,41 446,and 63 027 unigenes annotated,respectively.GO annotation categorized the genes into three major categories comprising 56 subcategories.KEGG pathway annotation identified 129 standard metabolic pathways,among which 23 were classified as secondary metabolic pathways.A total of 94 731 Coding Sequences (CDSs) were predicted,with the majority being short-length sequences.Simple Sequence Repeat (SSR) analysis identified 28 079 SSRs,with dinucleotide SSRs being the most abundant,accounting for 70.12% of the total SSRs.Single Nucleotide Polymorphism (SNP) analysis detected 23 139,21 246,28 280,55 409,and 17 084 SNPs in the leaves,petioles,leaf axes,roots,and rhizomes,respectively.Differential gene expression analysis between petioles and rhizomes identified 13 829 upregulated and 24 250 downregulated genes.GO functional enrichment analysis revealed that 226 differentially expressed genes related to the phenylpropanoid biosynthesis pathway were enriched in both petioles and rhizomes.This study provides transcriptomic data support for future in-depth investigations into the secondary metabolic pathways of D.crassirhizoma,particularly the biosynthesis of phloroglucinols and flavonoids, and related gene functions. |
| Key words: Dryopteris crassirhizoma transcriptome functional annotation metabolic pathways differentially expressed genes |
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