多花黄精种子微根茎基因表达特征分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-0115

生物技术通报 ›› 2023, Vol. 39 ›› Issue (8): 220-233.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0115

多花黄精种子微根茎基因表达特征分析

刘保财¹^,²(), 陈菁瑛¹^,²(), 张武君¹^,², 黄颖桢¹^,², 赵云青¹^,², 刘剑超³, 危智诚⁴

1.福建省农业科学院农业生物资源研究所，福州 350003
2.福建省农业科学院药用植物研究中心，福州 350003
3.福建省南平市邵武市农业农村局，邵武 354000
4.福建和平古镇农业开发有限公司，邵武 354000

收稿日期:2023-02-13 出版日期:2023-08-26 发布日期:2023-09-05
通讯作者: 陈菁瑛，女，研究员，研究方向：药用植物资源利用与规范栽培；E-mail: cjy6601@163.com
作者简介:刘保财，男，博士，助理研究员，研究方向：中草药繁殖、育种与栽培；E-mail: 626813844@qq.com
基金资助:
南平市科技局项目(N2020Y004);福建省人民政府协同创新工程项目(XTCXGC2021003);福建省农业科学院科技创新团队(CXTD2021014-2);“一带一路”国家传统草药实物库及图片信息库建设(2018FY100702)

Characteristics Analysis of Seed Microrhizome Gene Expression of Polygonatum cyrtonema

LIU Bao-cai¹^,²(), CHEN Jing-ying¹^,²(), ZHANG Wu-jun¹^,², HUANG Ying-zhen¹^,², ZHAO Yun-qing¹^,², LIU Jian-chao³, WEI Zhi-cheng⁴

1. Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou 350003
2. Research Center for Medicinal Plant, Fujian Academy of Agricultural Sciences, Fuzhou 350003
3. Agricultural and Rural Bureau of Shaowu City, Nanping City, Fujian Province, Shaowu 354000
4. Fujian Heping Ancient Town Agricultural Development Co., Ltd., Shaowu 354000

Received:2023-02-13 Published:2023-08-26 Online:2023-09-05

摘要/Abstract

摘要：

多花黄精种子发芽过程具有微根茎形成的特殊萌发现象，阐述微根茎形成过程中基因表达的变化有助于微根茎形态结构及其发育、种子生理等相关研究。本文通过高通量测序技术，对不同萌发状态的多花黄精种子进行转录组测序及生物信息分析。结果表明，微根茎形成时与胚根突破种皮共有显著性差异的Unigenes 17 907条，在代谢过程、催化活性、蛋白质磷酸化等Terms中均有较高的差异表达；Pathway显著性富集表明，差异基因主要富集于植物激素信号转导、淀粉和蔗糖代谢、黄酮类生物合成等通路中，且富集到植物激素信号转导通路中的基因有大量表达，尤其是油菜素内酯通路基因表达上调。微根茎变绿前后共有显著性差异的Unigenes 26 833条，主要富集在代谢过程、肽生物合成过程、催化活性等通路中；Pathway显著性富集表明，差异基因主要富集于核糖体、淀粉和蔗糖代谢、光合作用等通路中，在光合系统中几乎所有的关键酶均上调。该文明确了多花黄精种子微根茎的形成是系列基因复杂的调控网络，且油菜素内酯可能对微根茎的形成具有重要作用，微根茎变绿后即可进行光合作用，为微根茎形成的生理研究、生产上促进微根茎快速膨大、微根茎的开发利用等深入研究提供参考。

关键词: 多花黄精, 种子, 微根茎, 植物激素, 淀粉及蔗糖, 光合, 油菜素内酯

Abstract:

The germination process of Polygonatum cyrtonema seeds have a special germination phenomenon of micro rhizomes formation. The purpose of explaining the changes of key genes in the germination process is to lay a foundation for related research on seed physiology, morphological structure development and so on. In this paper, based on high-throughput sequencing technology, the transcriptome sequencing and bioinformatics analysis were performed on the seeds of P. cyrtonema in different germination states. The results showed that 17 907 differentially expressed genes were identified in microrhizome formation, compared to radicle breakthrough seed coat, these genes were in significantly different expressions in terms of metabolic process, catalytic activity, protein phosphorylation, etc. Pathway significance enrichment indicated that the differential genes were mainly enriched in plant hormone signal transduction, starch and sucrose metabolism, flavonoid biosynthesis, and other pathways. Genes enriched were abundantly expressed in plant hormone signal transduction pathways. Especially, the expression genes were up-regulated in brassinosteroid biosynthesis pathway. There were 26 833 significant differences Unigenes before and after the microrhizomes turned green, mainly enriched in metabolic process, peptide biosynthesis process, catalytic activity and other pathways. The differential genes were mainly enriched in, starch and sucrose metabolism, photosynthesis and other pathways by KEGG pathway enrichment analysis. The germination process of P. cyrtonema seeds is a complex regulatory network of a series of genes, and genes related with in brassinosteroid biosynthesis pathway may have an important role in the formation of microhizome. The results also provides a reference for in-depth research on the micro-rhizome formation physiology, micro-rhizome rapid expansion in production, and microhizom exploitation.

Key words: Polygonatum cyrtonema, seeds, microrhizome, plant hormone, starch and sucrose, photosynthesis, brassinosteroid

刘保财, 陈菁瑛, 张武君, 黄颖桢, 赵云青, 刘剑超, 危智诚. 多花黄精种子微根茎基因表达特征分析[J]. 生物技术通报, 2023, 39(8): 220-233.

LIU Bao-cai, CHEN Jing-ying, ZHANG Wu-jun, HUANG Ying-zhen, ZHAO Yun-qing, LIU Jian-chao, WEI Zhi-cheng. Characteristics Analysis of Seed Microrhizome Gene Expression of Polygonatum cyrtonema[J]. Biotechnology Bulletin, 2023, 39(8): 220-233.

图/表 14

图1 多花黄精种子萌发过程 A：胚根突破种皮；B：胚根伸长；C：胚轴膨大；D：微根状茎；E：绿色微根状茎；F：小苗；处于萌发阶段的A、D和E作为本试验的实验材料

Fig. 1 Germination process of P. cyrtonema seeds A: Radicle breaks through seed coat; B: radicle elongation; C: hypocotyl enlargement; D: microrhizomes; E: green microrhizomes; F: seedlings. A, D and E in germination stage were used as experimental materials in this experiment

表1 RT-qPCR引物序列

Table 1 Gene-specific primers used in RT-qPCR

基因 Gene	引物 Primer	序列 Sequence（5'-3'）
AUX1	Cluster-68615.91119-F	CCTCTCCTTCTTGGTCCTGTA
AUX1	Cluster-68615.91119-R	GGTGGCTCAACTTATGATGCT
AUX2	Cluster-68615.87861-F	TGCTCATCCATCAGTTCATAACC
AUX2	Cluster-68615.87861-R	GAATACGATTGCGAGGAACCATA
CH3	Cluster-58608.0-F	AAGAAGACCTCCAGAAGAGCATA
CH3	Cluster-58608.0-R	GACAATCTCCCAGAACAACACAT
TF	Cluster-68615.45537-F	CTTCCTGCTGCTTTCTCTTAGTG
TF	Cluster-68615.45537-R	TGCGGCTGCTCAGATTATTG
SnPK2	Cluster-68615.69985-F	ATGCTGATGACTCTGATTCTGATG
SnPK2	Cluster-68615.69985-R	GCCTACAACCGATACTTCTGATAC
MYC2	Cluster-68615.81195-F	AGATCAGCTCAGCTTCCATCA
MYC2	Cluster-68615.81195-R	CATTCCAGTTCCTTCGCCATT
β-glucosidase	Cluster-68615.43996-F	ACAAGGGTTAATGGGACTTCTCT
β-glucosidase	Cluster-68615.43996-R	CTGAAGAATCGCCTCCAAGTG
Actin	Actin_Cluster-F	CACCGATTGACACAAGGAGAG
Actin	Actin_Cluster-R	AGGATGGCTTACTACATTGACTTC

表2 各样品reads 与组装转录本比对

Table 2 Mapped results of sample reads and assembly transcripts

样品 Sample	总读长 Total reads/bp	总匹配数 Total mapped ones/bp
A1	40 179 174	29 824 074（74.23%）
A2	45 826 078	32 824 940（71.63%）
A3	44 560 782	32 498 548（72.93%）
D1	45 873 682	34 073 516（74.28%）
D2	41 999 498	31 537 406（75.09%）
D3	45 760 904	33 679 092（73.60%）
E1	41 290 430	30 888 404（74.81%）
E2	44 373 676	33 739 212（76.03%）
E3	44 063 488	33 299 498（75.57%）

表3 样品表达水平FPKM区间数量统计

Table 3 FPKM interval statistics of sample expressed levels

样品 Sample	FPKM 区间FPKM Interval
样品 Sample	0≤FPKM≤0.1	0.1<FPKM≤0.3	0.3<FPKM≤3.57	3.57<FPKM≤15	15<FPKM≤60	FPKM>60
A1	45 729（25.64%）	8 928（5.01%）	84 666（47.48%）	26 418（14.82%）	9 731（5.46%）	2 847（1.60%）
A2	90 461（50.73%）	4 155（2.33%）	46 585（26.12%）	25 282（14.18%）	8 776（4.92%）	3 060（1.72%）
A3	92 713（51.99%）	2 373（1.33%）	42 307（23.73%）	28 240（15.84%）	9 676（5.43%）	3 010（1.69%）
D1	68 567（38.45%）	14 059（7.88%）	64 246（36.03%）	19 173（10.75%）	9 466（5.31%）	2 808（1.57%）
D2	68 767（38.56%）	13 366（7.50%）	64 688（36.28%）	19 321（10.84%）	9 411（5.28%）	2 766（1.55%）
D3	69 033（38.71%）	13 351（7.49%）	64 127（35.96%）	19 404（10.88%）	9 570（5.37%）	2 834（1.59%）
E1	63 577（35.65%）	11 564（6.49%）	70 391（39.47%）	20 459（11.47%）	9 569（5.37%）	2 759（1.55%）
E2	61 068（34.25%）	13 276（7.45%）	72 028（40.39%）	19 855（11.13%）	9 390（5.27%）	2 702（1.52%）
E3	59 900（33.59%）	13 120（7.36%）	73 014（40.95%）	20 113（11.28%）	9 453（5.30%）	2 719（1.52%）

图2 DvsA差异表达基因

Fig. 2 DvsA different expressed genes A01: Protein phosphorylation. A02: Phosphorylation. A03: Phosphate-containing compound metabolic process. A04: Phosphorus metabolic process. A05: Metabolic process. A06: Oxidation-reduction process. A07: Microtubule-based movement. A08: Cellular carbohydrate metabolic process. A09: Carbohydrate metabolic process. A10: Negative regulation of translation. A11: Negative regulation of cellular amide metabolic process. A12: Cellular polysaccharide metabolic process. A13: Cellular protein modification process. A14: Protein modification process. A15: Microtubule. A16: Tubulin complex. A17: Apoplast. A18: Cell wall. A19: Catalytic activity. A20: Hydrolase activity, acting on glycosyl bonds. A21:Transferase activity. A22: Tetrapyrrole binding, A23: Heme binding. A24: Protein kinase activity. A25: Hydrolase activity, hydrolyzing O-glycosyl compounds. A26: RNA glycosylase activity. A27: rRNA N-glycosylase activity. A28: Hydrolase activity. A29: Phosphotransferase activity, alcohol group as acceptor. A30: Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. A31: Microtubule binding. A32: Kinase activity. A33: Transferase activity, transferring acyl groups other than amino-acyl groups. A34: Oxidoreductase activity. A35: Microtubule motor activity. A36: Ion binding. A37: Iron ion binding. A38: Tubulin binding. A39: Xyloglucan: xyloglucosyl transferase activity. A40: Transferase activity, transferring phosphorus-containing groups

图3 DvsA差异基因KEGG通路富集

Fig. 3 KEGG pathway enrichment of DvsA differential gene

图4 TOP 20 差异基因KEGG富集结果

Fig. 4 KEGG enrichment results of TOP 20 differential genes

图5 参与淀粉和蔗糖代谢的DvsA差异表达基因节点红色边框为包含上调差异基因，节点绿色边框为包含下调差异基因，节点黄色边框为包含上调和下调差异基因。下同

Fig. 5 DvsA differentially expressed genes involved in starch and sucrose metabolism The red border of the node contains up-regulated differential genes; the green border of the node contains the down-regulated differential genes; and the yellow border of the node contains the up-regulated and down-regulated differential genes. The same below

图6 参与植物激素信号转导的DvsA差异表达基因

Fig. 6 DvsA differentially expressed genes involved in plant hormone signal transduction

图7 EvsD差异表达基因

Fig. 7 EvsD differently expressed genes B01: Ribosome biogenesis. B02: Translation. B03: Ribonucleoprotein complex biogenesis. B04: Peptide biosynthetic process. B05: Peptide metabolic process. B06: Cellular amide metabolic process. B07: Amide biosynthetic process. B08: Oxidation-reduction process. B09: Organonitrogen compound biosynthetic process. B10: Organonitrogen compound metabolic process. B11: Cellular component biogenesis. B12: Protein metabolic process. B13: Metabolic process. B14: Cellular protein metabolic process. B15: Biosynthetic process. B16: Organic substance biosynthetic process. B17: Cellular macromolecule biosynthetic process. B18: Cellular component organization or biogenesis. B19: Macromolecule biosynthetic process. B20: Cellular nitrogen compound biosynthetic process. B21: Cellular biosynthetic process. B22: Single-organism metabolic process. B23: Obsolete peroxidase reaction. B24: Ribosome. B25: Ribonucleoprotein complex. B26: Non-membrane-bounded organelle. B27: Intracellular non-membrane-bounded organelle. B28: Cytoplasmic part. B29: Cytoplasm. B30: Macromolecular complex. B31: Structural constituent of ribosome. B32: Oxidoreductase activity. B33: Structural molecule activity. B34: Catalytic activity. B35: Antioxidant activity. B36: Oxidoreductase activity, acting on peroxide as acceptor. B37: Pyrophosphatase activity. B38: Peroxidase activity. B39: Nucleoside-triphosphatase activity. B40: GTPase activity.

图8 TOP 20差异基因KEGG富集结果

Fig. 8 KEGG enrichment results of TOP 20 differential genes

图9 TOP 20 EvsD差异表达基因KEGG富集

Fig. 10 KEGG enrichment results of TOP 20 EvsD differently expressed genes

图10 EvsD差异基因与ko00195通路匹配

Fig. 10 Map of EvsD differential gene in KEGG pathway ko00195

图11 7个差异基因的RT-qPCR验证蓝色线条图为转录组表达量，橙色柱状图为RT-qPCR表达量；不同小写字母代表同一基因在微根茎发育的不同形态表达量存在显著差异（P<0.05）

Fig. 11 Verification of seven selected DEGs by RT-qPCR Comparison of RNA-seq data（blue line chart）with RT-qPCR data（orange bar graph）. Different lowercase letters indicate significant differences in the expression levels of the same gene in different morphology of micro-rhizome development at 0.05 level

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多花黄精种子微根茎基因表达特征分析

Characteristics Analysis of Seed Microrhizome Gene Expression of Polygonatum cyrtonema

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