Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (10): 231-245.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0315
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XU Jun1(
), YE Yu-qing1, NIU Ya-jing2, HUANG He1(), ZHANG Meng-meng2()
Received:2023-04-08
Online:2023-10-26
Published:2023-11-28
Contact:
HUANG He, ZHANG Meng-meng
E-mail:1405549321@qq.com;101navy@163.com;mengmengzhang818@sina.com
XU Jun, YE Yu-qing, NIU Ya-jing, HUANG He, ZHANG Meng-meng. Transcriptome Analysis of Rhizome Development in Chrysanthemum× × morifolium[J]. Biotechnology Bulletin, 2023, 39(10): 231-245.
Fig. 1 Schematic diagram of ‘2017XS’ and ‘2005042’ rhizomes and schematic diagram of 8 transcriptome sampling A: Strain with rhizome‘2017XS’. B: Strain with rhizome‘2005042’. C: The material used for transcriptome sequencing is‘2017XS’. The blue circle indicates the specific part of the material, and the arrow indicates the details of the material. Ray florets were taken from the reproductive stage, and other materials were taken from the vegetative stage
| 基因名称Gene name | 基因序列号Gene ID | 正向引物序列Forward primer sequence（5'-3'） | 反向引物序列Reverse primer sequence（5'-3'） |
|---|---|---|---|
| LHY | c226991.graph_c0 | CGAAGACCGCAGTGCAAATC | TCCCATCCTTTTCTGCCACC |
| BG | c188673.graph_c0 | TGGTCTCGGTTGTTTTGCTTG | TGGAAATGAAGACGGAGTGGAA |
| bZIP | c208538.graph_c0 | GCAATACATATCGGAGCTAGAACG | GCAATCCTTTGCTTGAGGACAC |
| ABA8ox | c209725.graph_c0 | AAGCTCGTTCAAGGCTCGTTAT | TGAGTCCAAGGCGGAGACAG |
| UGT | c177448.graph_c0 | TAACAAGTATGGAAGGAGCAGGTG | GTGGATGGGATGGATGACGA |
| RLP | c217842.graph_c0 | GGATTTCGGGAATGCACTTACT | TCTAATGGAATCGGACCTGCTAAT |
Table 1 Primer sequences for RT-qPCR
| 基因名称Gene name | 基因序列号Gene ID | 正向引物序列Forward primer sequence（5'-3'） | 反向引物序列Reverse primer sequence（5'-3'） |
|---|---|---|---|
| LHY | c226991.graph_c0 | CGAAGACCGCAGTGCAAATC | TCCCATCCTTTTCTGCCACC |
| BG | c188673.graph_c0 | TGGTCTCGGTTGTTTTGCTTG | TGGAAATGAAGACGGAGTGGAA |
| bZIP | c208538.graph_c0 | GCAATACATATCGGAGCTAGAACG | GCAATCCTTTGCTTGAGGACAC |
| ABA8ox | c209725.graph_c0 | AAGCTCGTTCAAGGCTCGTTAT | TGAGTCCAAGGCGGAGACAG |
| UGT | c177448.graph_c0 | TAACAAGTATGGAAGGAGCAGGTG | GTGGATGGGATGGATGACGA |
| RLP | c217842.graph_c0 | GGATTTCGGGAATGCACTTACT | TCTAATGGAATCGGACCTGCTAAT |
Fig. 2 Unigene length distribution and functional annotation and classification of DEGs in rhizomes A: The distribution of Unigene in different lengths in transcriptome. The X-axis represents the length of Unigene, and the Y-axis represents the number of Unigenes at different lengths. B: Histogram of KOG classification. Unigenes with significant matches in the KOG database are classified into 25 categories. Histograms of different colors represent different KOG categories, and Y-axis represent the number of genes. C: Classification of Unigenes in KEGG pathways. The pink histogram represents the Cellular Process, the yellow histogram represents the Environmental Information Process, the dark green histogram represents the Genetic Information Process, the light green histogram represents the Metabolism, and the blue histogram represents the Organismal system. The number represents the number of genes in this KEGG category and the percentage of the number of genes in this category in the total number of genes
Fig. 3 WGCNA analysis A: Clustering dendrograms of genes and module division. The upper part is the genes cluster dendrograms, the lower part is assigned module, and the same modules had the same color. B: Heat map of the correlation between co-expressed modules and‘2017XS’ tissues. Each row represents a module, and each column represents a tissue. The number in the rectangular box represents the correlation coefficient and corresponding P-value between the module and the trait. Red block represents the positive correlation between the module and the tissues, and blue represents the negative correlation. RH: rhizome apical; RT: middle of rhizome; RB: bottle of rhizome; SA: shoot apical; L: leaf; S: shoot; R: root; F: ray floret
| 差异基因筛选方式 Screening method of DEGs | 基因 Gene | 功能注释 Functional annotation | FPKM | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 根状茎尖 Rhizome tip | 根状茎中部 Rhizome middle | 根状茎下部 Rhizome bottom | 茎尖 Shoot apical | 叶片 Leaf | 茎段 Stem | 根系 Root | 舌状花 Ray floret | |||
| WGCNA | PME68（c195055.graph_c0） | Probable pectinesterase 68（Artemisia annua） | 23.06 | 4.01 | 0.19 | 6.81 | 0.12 | 0.35 | 3.85 | 0.06 |
| PHYB（c200625.graph_c0） | Phytochrome B（Artemisia annua） | 5.83 | 1.45 | 0.57 | 1.18 | 0 | 0.58 | 0 | 0.85 | |
| FLA7（c216061.graph_c0） | Fasciclin-like arabinogalactan protein 7（Tanacetum cinerariifolium） | 71.37 | 7.08 | 0.08 | 14.25 | 4.05 | 9.19 | 0.02 | 19.08 | |
| LEA1（c165828.graph_c1） | Late embryogenesis abundant protein 1（Artemisia annua） | 295.49 | 72.99 | 9.25 | 0.34 | 0.73 | 0 | 0 | 0 | |
| OLE（c190721.graph_c0） | Oleosin（Artemisia annua） | 5.17 | 1.52 | 0.24 | 0.7 | 0.04 | 0.21 | 0 | 0.81 | |
| TIP2-1（c156293.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 24.91 | 2.7 | 0.29 | 0 | 0 | 0.32 | 0 | 0.32 | |
| LIL3.1（c197767.graph_c1） | Light-harvesting complex-like protein 3 isotype 1（Helianthus annuus） | 7.43 | 0.18 | 0.15 | 0.17 | 0.22 | 0.15 | 0.82 | 0.03 | |
| ABA8ox（c209725.graph_c0） | ABA 8-oxidase（Artemisia annua） | 12.55 | 1.35 | 0.27 | 0.68 | 0.39 | 2.05 | 0.1 | 1.04 | |
| TIP1-1（c185069.graph_c0） | Aquaporin TIP1-1（Artemisia annua） | 503.78 | 74.87 | 6.23 | 51.4 | 32.75 | 21.61 | 0.04 | 6.6 | |
| RD21A（c208052.graph_c0） | Cysteine proteinase COT44（Tanacetum cinerariifolium） | 13.76 | 1.99 | 1.56 | 0.98 | 0.28 | 1.71 | 0.12 | 0.37 | |
| ARP1（c197835.graph_c0） | Probable RNA-binding protein ARP1 isoform X2（Tanacetum cinerariifolium） | 10.34 | 0.74 | 0.07 | 1.05 | 0 | 0.95 | 0 | 0.13 | |
| ARP1（c197835.graph_c1） | Probable RNA-binding protein ARP1 isoform X2（Helianthus annuus） | 50.65 | 6.38 | 0.65 | 4.54 | 0.05 | 5.96 | 0.1 | 0.95 | |
| TIP2-1（c181494.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 13.52 | 0.95 | 0.16 | 0 | 0 | 0 | 0 | 0 | |
| bZIP34（c208538.graph_c0） | Basic leucine zipper 34（Artemisia annua） | 41.51 | 11.57 | 0.27 | 2.55 | 2.05 | 7.91 | 0 | 2.58 | |
| HIDH（c211020.graph_c0） | 2-hydroxyisoflavanone dehydratase-like（Erigeron canadensis） | 7.48 | 1.18 | 1.16 | 1.96 | 0.08 | 1.97 | 2.16 | 0.03 | |
| VENN | DREB2F（c193648.graph_c0） | Dehydration-responsive element-binding protein 2F（Tanacetum cinerariifolium） | 3.13 | 0.03 | 0.03 | 0.38 | 0 | 0 | 0 | 0 |
| CZF2（c195263.graph_c0） | Zinc finger, CCCH-type（Artemisia annua） | 4.12 | 0.99 | 0.95 | 0.3 | 0.3 | 0.24 | 0.06 | 0.2 | |
| ABA8ox4（c212882.graph_c0） | Abscisic acid 8’-hydroxylase 4（Tanacetum cinerariifolium） | 3.72 | 0.63 | 0.07 | 0.11 | 0.7 | 0.72 | 0.12 | 0.06 | |
| PP2C38（c204872.graph_c0） | Probable protein phosphatase 2C 38（Artemisia annua） | 5.27 | 0.08 | 0.02 | 0.16 | 0.7 | 0 | 0.02 | 0.16 | |
| UGT83A1（c177448.graph_c0） | UDP-glucosyltransferase（Artemisia annua） | 2.8 | 0.06 | 0.1 | 0.25 | 0.23 | 0.05 | 0 | 0 | |
Table 2 Summary of highly expressed genes in the rhizome apical of 2017XS
| 差异基因筛选方式 Screening method of DEGs | 基因 Gene | 功能注释 Functional annotation | FPKM | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 根状茎尖 Rhizome tip | 根状茎中部 Rhizome middle | 根状茎下部 Rhizome bottom | 茎尖 Shoot apical | 叶片 Leaf | 茎段 Stem | 根系 Root | 舌状花 Ray floret | |||
| WGCNA | PME68（c195055.graph_c0） | Probable pectinesterase 68（Artemisia annua） | 23.06 | 4.01 | 0.19 | 6.81 | 0.12 | 0.35 | 3.85 | 0.06 |
| PHYB（c200625.graph_c0） | Phytochrome B（Artemisia annua） | 5.83 | 1.45 | 0.57 | 1.18 | 0 | 0.58 | 0 | 0.85 | |
| FLA7（c216061.graph_c0） | Fasciclin-like arabinogalactan protein 7（Tanacetum cinerariifolium） | 71.37 | 7.08 | 0.08 | 14.25 | 4.05 | 9.19 | 0.02 | 19.08 | |
| LEA1（c165828.graph_c1） | Late embryogenesis abundant protein 1（Artemisia annua） | 295.49 | 72.99 | 9.25 | 0.34 | 0.73 | 0 | 0 | 0 | |
| OLE（c190721.graph_c0） | Oleosin（Artemisia annua） | 5.17 | 1.52 | 0.24 | 0.7 | 0.04 | 0.21 | 0 | 0.81 | |
| TIP2-1（c156293.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 24.91 | 2.7 | 0.29 | 0 | 0 | 0.32 | 0 | 0.32 | |
| LIL3.1（c197767.graph_c1） | Light-harvesting complex-like protein 3 isotype 1（Helianthus annuus） | 7.43 | 0.18 | 0.15 | 0.17 | 0.22 | 0.15 | 0.82 | 0.03 | |
| ABA8ox（c209725.graph_c0） | ABA 8-oxidase（Artemisia annua） | 12.55 | 1.35 | 0.27 | 0.68 | 0.39 | 2.05 | 0.1 | 1.04 | |
| TIP1-1（c185069.graph_c0） | Aquaporin TIP1-1（Artemisia annua） | 503.78 | 74.87 | 6.23 | 51.4 | 32.75 | 21.61 | 0.04 | 6.6 | |
| RD21A（c208052.graph_c0） | Cysteine proteinase COT44（Tanacetum cinerariifolium） | 13.76 | 1.99 | 1.56 | 0.98 | 0.28 | 1.71 | 0.12 | 0.37 | |
| ARP1（c197835.graph_c0） | Probable RNA-binding protein ARP1 isoform X2（Tanacetum cinerariifolium） | 10.34 | 0.74 | 0.07 | 1.05 | 0 | 0.95 | 0 | 0.13 | |
| ARP1（c197835.graph_c1） | Probable RNA-binding protein ARP1 isoform X2（Helianthus annuus） | 50.65 | 6.38 | 0.65 | 4.54 | 0.05 | 5.96 | 0.1 | 0.95 | |
| TIP2-1（c181494.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 13.52 | 0.95 | 0.16 | 0 | 0 | 0 | 0 | 0 | |
| bZIP34（c208538.graph_c0） | Basic leucine zipper 34（Artemisia annua） | 41.51 | 11.57 | 0.27 | 2.55 | 2.05 | 7.91 | 0 | 2.58 | |
| HIDH（c211020.graph_c0） | 2-hydroxyisoflavanone dehydratase-like（Erigeron canadensis） | 7.48 | 1.18 | 1.16 | 1.96 | 0.08 | 1.97 | 2.16 | 0.03 | |
| VENN | DREB2F（c193648.graph_c0） | Dehydration-responsive element-binding protein 2F（Tanacetum cinerariifolium） | 3.13 | 0.03 | 0.03 | 0.38 | 0 | 0 | 0 | 0 |
| CZF2（c195263.graph_c0） | Zinc finger, CCCH-type（Artemisia annua） | 4.12 | 0.99 | 0.95 | 0.3 | 0.3 | 0.24 | 0.06 | 0.2 | |
| ABA8ox4（c212882.graph_c0） | Abscisic acid 8’-hydroxylase 4（Tanacetum cinerariifolium） | 3.72 | 0.63 | 0.07 | 0.11 | 0.7 | 0.72 | 0.12 | 0.06 | |
| PP2C38（c204872.graph_c0） | Probable protein phosphatase 2C 38（Artemisia annua） | 5.27 | 0.08 | 0.02 | 0.16 | 0.7 | 0 | 0.02 | 0.16 | |
| UGT83A1（c177448.graph_c0） | UDP-glucosyltransferase（Artemisia annua） | 2.8 | 0.06 | 0.1 | 0.25 | 0.23 | 0.05 | 0 | 0 | |
| 差异基因 筛选方式 Screening method of DEGs | 基因序列号 Gene ID | 功能注释 Functional annotation | FPKM | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 根状茎尖 Rhizome tip | 根状茎中部 Rhizome middle | 根状茎下部 Rhizome bottom | 茎尖 Shoot apical | 叶片 Leaf | 茎段 Stem | 根系 Root | 舌状花 Ray floret | |||
| WGCNA | TFL1（c181499.graph_c0） | TFL1-like protein（Chrysanthemum x morifolium） | 6.19 | 14.30 | 1.24 | 0.14 | 0.20 | 0.07 | 0.17 | 0.04 |
| UVR8（c225307.graph_c0） | Ultraviolet-B receptor UVR8 isoform X2（Cynara cardunculus） | 24.60 | 21.64 | 27.53 | 1.41 | 1.62 | 1.30 | 0.74 | 1.52 | |
| GWD（c220138.graph_c0） | Alpha-glucan water dikinase 1（Helianthus annuus） | 31.29 | 22.66 | 22.05 | 7.28 | 5.81 | 0.10 | 4.84 | 4.22 | |
| UGT73C3（c193961.graph_c0） | UDP-glucosyl transferase 73B2（Lactuca sativa） | 11.45 | 24.51 | 12.62 | 1.14 | 0.49 | 0.65 | 2.62 | 0.32 | |
| LEA1（c165828.graph_c1） | Late embryogenesis abundant protein 1（Artemisia annua） | 295.49 | 72.99 | 9.25 | 0.34 | 0.73 | 0 | 0 | 0 | |
| LEA Dc3（c195245.graph_c0） | Late embryogenesis abundant protein Dc3（Artemisia annua） | 3668.15 | 3341 | 1742.08 | 13.18 | 8.53 | 2.06 | 16.2 | 9.52 | |
| zinc finger（c171393.graph_c0） | Zinc finger, CCHC-type（Artemisia annua） | 1.82 | 15.18 | 3.16 | 0 | 0 | 0.29 | 0.99 | 0.51 | |
| RLP7（c217842.graph_c0） | Leucine-rich repeat protein（Artemisia annua） | 14.87 | 9.42 | 2.48 | 0.02 | 0.07 | 0.09 | 0.13 | 0 | |
| ERF098（c180295.graph_c0） | Ethylene-responsive transcription factor ERF098（Lactuca sativa） | 3.51 | 3.40 | 2.77 | 0.88 | 0.41 | 0 | 0.48 | 0 | |
| PIP1-1（c215772.graph_c0） | Aquaporin PIP1-1-like（Artemisia annua） | 343.98 | 533.32 | 370.29 | 44.36 | 10.71 | 48.83 | 15.59 | 32.56 | |
| hAT transposon（c228735.graph_c0） | Putative hAT transposon superfamily（Tanacetum cinerariifolium） | 895.49 | 1500.66 | 580.71 | 95.56 | 57.82 | 32.38 | 158.83 | 76.66 | |
| GH1（c176119.graph_c0） | Glycoside hydrolase family 1（Artemisia annua） | 12.04 | 27.68 | 15.34 | 0 | 0.13 | 1.02 | 3.03 | 0.73 | |
| SAMDC（c206787.graph_c0） | S-adenosylmethionine decarboxylase proenzyme（Artemisia annua） | 88.53 | 53.73 | 22.24 | 2.34 | 1.76 | 1.26 | 2.14 | 1.16 | |
| LNK1（c223971.graph_c0） | Protein LNK1-like isoform X1（Lactuca sativa） | 14.82 | 14.45 | 16.06 | 1.13 | 0.59 | 1.93 | 0.32 | 0.41 | |
| LHY（c226991.graph_c0） | Late elongated hypocotyl-like（Chrysanthemum seticuspe f. boreale） | 55.07 | 59.39 | 47.02 | 11.46 | 6.01 | 8.76 | 4.67 | 12.26 | |
| TIP2-1（c181494.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 13.52 | 0.95 | 0.16 | 0 | 0 | 0 | 0 | 0 | |
| RE1（c213815.graph_c1） | Putative RNA-directed DNA polymerase（Helianthus annuus） | 14.31 | 9.52 | 8.36 | 1.19 | 0.32 | 1.76 | 1.61 | 0.38 | |
| BG 46（c188673.graph_c0） | Beta glucosidase 46（Artemisia annua） | 5.00 | 7.08 | 7.03 | 0.15 | 0.80 | 0 | 0.11 | 0 | |
| ACA8（c226840.graph_c0） | Calcium-transporPting ATPase 8（Erigeron canadensis） | 65.4 | 106.47 | 58.25 | 12.76 | 6.78 | 8.67 | 14.69 | 16.91 | |
| DREB1D（c212875.graph_c0） | Dehydration-responsive element-binding factor 1（Artemisia annua） | 13.93 | 8.66 | 2.94 | 0.16 | 0 | 0.04 | 0.25 | 0.13 | |
| MLP43（c91334.graph_c0） | MLP-like protein 43（Tanacetum cinerariifolium） | 128.75 | 232.78 | 41.83 | 8.21 | 0 | 1.35 | 9.98 | 3.82 | |
| K-means | LEA14（c204348.graph_c0） | Late embryogenesis abundant protein（Artemisia annua） | 972.25 | 411.65 | 189.58 | 2.30 | 4.40 | 0.19 | 12.78 | 5.00 |
| ACA10（c210148.graph_c0） | Calcium-transporting ATPase 10（Tanacetum cinerariifolium） | 60.68 | 126.95 | 65.40 | 13.2 | 4.11 | 8.93 | 16.34 | 19.69 | |
| LYK4（c215208.graph_c1） | LysM domain receptor-like kinase 4（Tanacetum cinerariifolium） | 26.77 | 49.34 | 43.47 | 1.80 | 1.66 | 6.83 | 7.13 | 0.44 | |
| PDC2（c187399.graph_c0） | Pyruvate decarboxylase 2（Tanacetum cinerariifolium） | 1.05 | 8.54 | 5.68 | 0 | 0.12 | 0 | 0 | 0 | |
| UGT73（c215576.graph_c0） | UDP-glycosyltransferase 73C7-like（Cynara cardunculus） | 29.51 | 59.45 | 37.95 | 3.22 | 2.8 | 2.83 | 5.55 | 1.07 | |
| zinc finger（c193154.graph_c0） | Zinc finger, CCHC-type（Artemisia annua） | 13.11 | 17.47 | 14.45 | 2.30 | 0.10 | 0.29 | 3.16 | 1.62 | |
| UVR8（c192386.graph_c0） | Ultraviolet-B receptor UVR8-like isoform X1（Erigeron canadensis） | 19.07 | 21.94 | 29.46 | 0.41 | 0.45 | 0.63 | 0 | 0 | |
| 1-SST（c222090.graph_c0） | Sucrose:sucrose 1-fructosyl transferase（Artemisia annua） | 1005.96 | 2853.86 | 1238.04 | 1.80 | 4.62 | 16.83 | 79.72 | 297.35 | |
| MLP43（c195694.graph_c0） | MLP-like protein 43（Artemisia annua） | 2035.38 | 5638.39 | 3866.43 | 224.77 | 17.43 | 77.31 | 669.73 | 75.88 | |
| COL12（c204664.graph_c0） | B-box zinc finger protein 32（Artemisia annua） | 2.50 | 3.98 | 4.90 | 0.14 | 0 | 0 | 0.08 | 0 | |
| VENN | CZF4（c195263.graph_c0） | Zinc finger, CCCH-type（Artemisia annua） | 4.12 | 0.99 | 0.95 | 0.30 | 0.30 | 0.06 | 0.24 | 0.20 |
| ERF C3（c195922.graph_c0） | Ethylene-response factor C3（Helianthus annuus） | 1.13 | 4.14 | 8.48 | 0 | 0 | 0.27 | 0.20 | 0.04 | |
| NDA1（c208704.graph_c0） | NADH dehydrogenase（Artemisia annua） | 1.63 | 1.43 | 3.08 | 0.21 | 0.06 | 0 | 0.46 | 0.27 | |
| BG 46（c196303.graph_c0） | Putative beta-glucosidase（Helianthus annuus） | 1.54 | 3.26 | 1.97 | 0.06 | 0.06 | 0.18 | 0.39 | 0.03 | |
| LEA Dc3（c208154.graph_c0） | Late embryogenesis abundant protein Dc3（Artemisia annua） | 0.19 | 2.36 | 51.39 | 0.05 | 0 | 0.04 | 0 | 0 | |
Table 3 Summary of highly expressed genes in the rhizomes of ‘2017XS’
| 差异基因 筛选方式 Screening method of DEGs | 基因序列号 Gene ID | 功能注释 Functional annotation | FPKM | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 根状茎尖 Rhizome tip | 根状茎中部 Rhizome middle | 根状茎下部 Rhizome bottom | 茎尖 Shoot apical | 叶片 Leaf | 茎段 Stem | 根系 Root | 舌状花 Ray floret | |||
| WGCNA | TFL1（c181499.graph_c0） | TFL1-like protein（Chrysanthemum x morifolium） | 6.19 | 14.30 | 1.24 | 0.14 | 0.20 | 0.07 | 0.17 | 0.04 |
| UVR8（c225307.graph_c0） | Ultraviolet-B receptor UVR8 isoform X2（Cynara cardunculus） | 24.60 | 21.64 | 27.53 | 1.41 | 1.62 | 1.30 | 0.74 | 1.52 | |
| GWD（c220138.graph_c0） | Alpha-glucan water dikinase 1（Helianthus annuus） | 31.29 | 22.66 | 22.05 | 7.28 | 5.81 | 0.10 | 4.84 | 4.22 | |
| UGT73C3（c193961.graph_c0） | UDP-glucosyl transferase 73B2（Lactuca sativa） | 11.45 | 24.51 | 12.62 | 1.14 | 0.49 | 0.65 | 2.62 | 0.32 | |
| LEA1（c165828.graph_c1） | Late embryogenesis abundant protein 1（Artemisia annua） | 295.49 | 72.99 | 9.25 | 0.34 | 0.73 | 0 | 0 | 0 | |
| LEA Dc3（c195245.graph_c0） | Late embryogenesis abundant protein Dc3（Artemisia annua） | 3668.15 | 3341 | 1742.08 | 13.18 | 8.53 | 2.06 | 16.2 | 9.52 | |
| zinc finger（c171393.graph_c0） | Zinc finger, CCHC-type（Artemisia annua） | 1.82 | 15.18 | 3.16 | 0 | 0 | 0.29 | 0.99 | 0.51 | |
| RLP7（c217842.graph_c0） | Leucine-rich repeat protein（Artemisia annua） | 14.87 | 9.42 | 2.48 | 0.02 | 0.07 | 0.09 | 0.13 | 0 | |
| ERF098（c180295.graph_c0） | Ethylene-responsive transcription factor ERF098（Lactuca sativa） | 3.51 | 3.40 | 2.77 | 0.88 | 0.41 | 0 | 0.48 | 0 | |
| PIP1-1（c215772.graph_c0） | Aquaporin PIP1-1-like（Artemisia annua） | 343.98 | 533.32 | 370.29 | 44.36 | 10.71 | 48.83 | 15.59 | 32.56 | |
| hAT transposon（c228735.graph_c0） | Putative hAT transposon superfamily（Tanacetum cinerariifolium） | 895.49 | 1500.66 | 580.71 | 95.56 | 57.82 | 32.38 | 158.83 | 76.66 | |
| GH1（c176119.graph_c0） | Glycoside hydrolase family 1（Artemisia annua） | 12.04 | 27.68 | 15.34 | 0 | 0.13 | 1.02 | 3.03 | 0.73 | |
| SAMDC（c206787.graph_c0） | S-adenosylmethionine decarboxylase proenzyme（Artemisia annua） | 88.53 | 53.73 | 22.24 | 2.34 | 1.76 | 1.26 | 2.14 | 1.16 | |
| LNK1（c223971.graph_c0） | Protein LNK1-like isoform X1（Lactuca sativa） | 14.82 | 14.45 | 16.06 | 1.13 | 0.59 | 1.93 | 0.32 | 0.41 | |
| LHY（c226991.graph_c0） | Late elongated hypocotyl-like（Chrysanthemum seticuspe f. boreale） | 55.07 | 59.39 | 47.02 | 11.46 | 6.01 | 8.76 | 4.67 | 12.26 | |
| TIP2-1（c181494.graph_c0） | Aquaporin TIP2-1（Tanacetum cinerariifolium） | 13.52 | 0.95 | 0.16 | 0 | 0 | 0 | 0 | 0 | |
| RE1（c213815.graph_c1） | Putative RNA-directed DNA polymerase（Helianthus annuus） | 14.31 | 9.52 | 8.36 | 1.19 | 0.32 | 1.76 | 1.61 | 0.38 | |
| BG 46（c188673.graph_c0） | Beta glucosidase 46（Artemisia annua） | 5.00 | 7.08 | 7.03 | 0.15 | 0.80 | 0 | 0.11 | 0 | |
| ACA8（c226840.graph_c0） | Calcium-transporPting ATPase 8（Erigeron canadensis） | 65.4 | 106.47 | 58.25 | 12.76 | 6.78 | 8.67 | 14.69 | 16.91 | |
| DREB1D（c212875.graph_c0） | Dehydration-responsive element-binding factor 1（Artemisia annua） | 13.93 | 8.66 | 2.94 | 0.16 | 0 | 0.04 | 0.25 | 0.13 | |
| MLP43（c91334.graph_c0） | MLP-like protein 43（Tanacetum cinerariifolium） | 128.75 | 232.78 | 41.83 | 8.21 | 0 | 1.35 | 9.98 | 3.82 | |
| K-means | LEA14（c204348.graph_c0） | Late embryogenesis abundant protein（Artemisia annua） | 972.25 | 411.65 | 189.58 | 2.30 | 4.40 | 0.19 | 12.78 | 5.00 |
| ACA10（c210148.graph_c0） | Calcium-transporting ATPase 10（Tanacetum cinerariifolium） | 60.68 | 126.95 | 65.40 | 13.2 | 4.11 | 8.93 | 16.34 | 19.69 | |
| LYK4（c215208.graph_c1） | LysM domain receptor-like kinase 4（Tanacetum cinerariifolium） | 26.77 | 49.34 | 43.47 | 1.80 | 1.66 | 6.83 | 7.13 | 0.44 | |
| PDC2（c187399.graph_c0） | Pyruvate decarboxylase 2（Tanacetum cinerariifolium） | 1.05 | 8.54 | 5.68 | 0 | 0.12 | 0 | 0 | 0 | |
| UGT73（c215576.graph_c0） | UDP-glycosyltransferase 73C7-like（Cynara cardunculus） | 29.51 | 59.45 | 37.95 | 3.22 | 2.8 | 2.83 | 5.55 | 1.07 | |
| zinc finger（c193154.graph_c0） | Zinc finger, CCHC-type（Artemisia annua） | 13.11 | 17.47 | 14.45 | 2.30 | 0.10 | 0.29 | 3.16 | 1.62 | |
| UVR8（c192386.graph_c0） | Ultraviolet-B receptor UVR8-like isoform X1（Erigeron canadensis） | 19.07 | 21.94 | 29.46 | 0.41 | 0.45 | 0.63 | 0 | 0 | |
| 1-SST（c222090.graph_c0） | Sucrose:sucrose 1-fructosyl transferase（Artemisia annua） | 1005.96 | 2853.86 | 1238.04 | 1.80 | 4.62 | 16.83 | 79.72 | 297.35 | |
| MLP43（c195694.graph_c0） | MLP-like protein 43（Artemisia annua） | 2035.38 | 5638.39 | 3866.43 | 224.77 | 17.43 | 77.31 | 669.73 | 75.88 | |
| COL12（c204664.graph_c0） | B-box zinc finger protein 32（Artemisia annua） | 2.50 | 3.98 | 4.90 | 0.14 | 0 | 0 | 0.08 | 0 | |
| VENN | CZF4（c195263.graph_c0） | Zinc finger, CCCH-type（Artemisia annua） | 4.12 | 0.99 | 0.95 | 0.30 | 0.30 | 0.06 | 0.24 | 0.20 |
| ERF C3（c195922.graph_c0） | Ethylene-response factor C3（Helianthus annuus） | 1.13 | 4.14 | 8.48 | 0 | 0 | 0.27 | 0.20 | 0.04 | |
| NDA1（c208704.graph_c0） | NADH dehydrogenase（Artemisia annua） | 1.63 | 1.43 | 3.08 | 0.21 | 0.06 | 0 | 0.46 | 0.27 | |
| BG 46（c196303.graph_c0） | Putative beta-glucosidase（Helianthus annuus） | 1.54 | 3.26 | 1.97 | 0.06 | 0.06 | 0.18 | 0.39 | 0.03 | |
| LEA Dc3（c208154.graph_c0） | Late embryogenesis abundant protein Dc3（Artemisia annua） | 0.19 | 2.36 | 51.39 | 0.05 | 0 | 0.04 | 0 | 0 | |
Fig. 4 Venn diagram of DEGs in three parts of rhizome and other tissues A: DEGs between rhizome tip and non-rhizome tissues. B: DEGs between middle of rhizome and non-rhizome tissues. C: DEGs between bottle of rhizome and non-rhizome tissues. Sets of different colors represent different comparison groups, and numbers represent the number of genes contained in the region. The red box indicates the genes differentially expressed in the five comparison groups. RH: rhizome apical; RT: middle of rhizome; RB: bottle of rhizome; SA: shoot apical; L: leaf; S: shoot; R: root; F: ray floret
Fig. 5 Cluster analysis of gene expression patterns of rhizome stable line ‘2017XS’ The X-axis of each cluster represents the material sequencing organization of the transcriptome, the Y-axis represents the gene expression level in the cluster, and the curve represents the change trend of gene expression level in the cluster. RH: rhizome apical; RT: middle of rhizome; RB: bottle of rhizome; SA: shoot apical; L: leaf; S: shoot; R: root; F: ray floret
Fig. 6 Verification of transcriptome sequencing data A: RT-qPCR verification of transcriptome-screened genes in ‘2017XS’. B: RT-qPCR verification of transcriptome-screened genes in‘2005042’. RH: rhizome apical; RT: middle of rhizome; RB: bottle of rhizome; SA: shoot apical; L: leaf; S: shoot; R: root; F: ray floret
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