Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea
Abstract
:1. Introduction
2. Results
2.1. Comparison of Morphological Phenotypes among Mustards
2.2. Identification of Differential Expression of Genes with RNA-Seq
2.3. K-Means Cluster and Enrichment Analyses of DEGs Associated with the Formation of Different Phenotypes
2.4. Differential Accumulation of Metabolites in Four Mustards
2.5. Conjoint Analysis of Genes and Metabolites Related to Purple Leaf Veins and Notched Leaves
2.6. Integrating Related Genes and Metabolites in the Flavonoid Biosynthesis Pathway Provides Insights into Purple Vein Formation
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. RNA Sequencing and Data Analysis
4.3. Metabolic Analysis
4.4. Combined Analysis of DEGs and DAMs
4.5. qRT-PCR Validation of RNA-Seq Results
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Samples | Raw Reads | Clean Reads | Q30 (%) | GC Content (%) | Unique Mapped |
---|---|---|---|---|---|
44-1 | 52,764,138 | 51,838,932 | 90.47 | 47.65 | 41,712,627 (80.47%) |
44-2 | 57,898,070 | 56,684,510 | 92.36 | 47.71 | 46,074,374 (81.28%) |
44-3 | 48,686,530 | 47,839,794 | 92.77 | 47.59 | 38,895,911 (81.30%) |
45-1 | 59,411,784 | 58,048,268 | 92.23 | 47.75 | 47,126,857 (81.19%) |
45-2 | 59,141,800 | 57,661,630 | 92.14 | 47.56 | 45,972,841 (79.73%) |
45-3 | 52,856,618 | 51,892,220 | 92.01 | 47.64 | 41,742,258 (80.44%) |
65-1 | 59,045,222 | 57,784,616 | 92.21 | 47.37 | 46,641,623 (80.72%) |
65-2 | 52,647,580 | 51,702,172 | 91.46 | 47.61 | 41,756,075 (80.76%) |
65-3 | 57,451,232 | 56,518,720 | 92.24 | 47.45 | 45,650,258 (80.77%) |
66-1 | 54,027,590 | 53,162,134 | 92.64 | 47.86 | 42,963,193 (80.82%) |
66-2 | 56,428,334 | 55,492,792 | 92.28 | 47.8 | 44,569,467 (80.32%) |
66-3 | 51,296,644 | 50,462,792 | 92.09 | 47.62 | 40,610,737 (80.48%) |
Metabolome ID | Compounds | Class I | Class II | Log2FC (45 vs. 44) | Log2FC (65 vs. 66) |
---|---|---|---|---|---|
CWJP002833 | Kaempferol-di-O-malonyl-glucoside-O-malonyl-diglucoside | Flavonoids | Flavonols | 13.84 | 1.64 |
Hmgp006596 | Cyclobrassinin | Alkaloids | Plumerane | 1.128 | 1.64 |
Hmyn007168 | LysoPG(16:0) | Lipids | Glycerol ester | 1.32 | 1.09 |
Lmmp002995 | Quercetin glu-malonyl-glucoside2 | Flavonoids | Flavonols | 12.68 | 12.25 |
Lmyn001269 | Kaempferol 3-O-β-D-sophoroside | Flavonoids | Flavonols | 1.03 | 12.34 |
mws0126 | 1-Stearoyl-sn-glycero-3-phosphocholine | Lipids | LPC | 1.156 | 1.72 |
mws0183 | Protocatechuic acid | Flavonoids | Flavanols | 1.63 | 1.70 |
mws0639 | 2,3-Dihydroxybenzoic acid | Organic acids | Organic acids | 1.18 | 1.10 |
mws1138 | Betanin | Alkaloids | Alkaloids | 14.19 | 13.17 |
pmb0876 | LysoPE 16:0 | Lipids | LPE | 1.68 | 1.74 |
pmb2936 | Disinapoyl hexoside | Phenolic acids | Phenolic acids | 1.76 | 12.55 |
pmb2940 | 1-O-β-D-Glucopyranosyl sinapate | Phenolic acids | Phenolic acids | 1.66 | 1.97 |
pmd0136 | LysoPC 18:0 | Lipids | LPC | 1.05 | 1.73 |
pmn001409 | Plantainoside A | Phenolic acids | Phenolic acids | 1.32 | 1.06 |
pmp001277 | 3-{(2-Aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl palmitate | Alkaloids | Alkaloids | 1.69 | 1.68 |
pmp001286 | LysoPC(18:0) | Lipids | LPC | 1.15 | 1.67 |
Hmpp002612 | Luteolin-7-O-β-D-gentiobioside | Flavonoids | Flavonoid | −2.19 | −1.31 |
Lmbp002592 | Kaempferol-3,7-di-O-β-D-glucopyranoside | Flavonoids | Flavonols | −2.34 | −1.82 |
mws0170 | Cyanidin chloride | Flavonoids | Anthocyanins | −2.26 | −2.32 |
pme0256 | Xanthine | Nucleotides and derivatives | Nucleotides and derivatives | −1.01 | −1.09 |
pme0516 | Inositol | Others | Saccharides and Alcohols | −1.66 | −2.42 |
Metabolome ID | Compounds | Class I | Class II | Log2FC (45 vs. 44) | Log2FC (45 vs. 66) |
---|---|---|---|---|---|
Cmln000394 | 4-(Methylthio)-3-OH-butyl glucosinolate (glucoraphanin) | Others | Glucosinolates | 1.41 | 1.37 |
CMLN000400 | 4-Methylsulfinyl-3-butenyl thioglucoside (glucoraphenin) | Others | Glucosinolates | 1.83 | 1.33 |
GQ512003 | Fer-agmatine | Alkaloids | Phenolamine | 1.25 | 3.54 |
Hmgp006596 | Cyclobrassinin | Alkaloids | Plumerane | 1.13 | 1.86 |
mws0997 | Petunidin 3-O-glucoside | Flavonoids | Anthocyanins | 2.00 | 1.04 |
pmb0489 | N-hexosyl-p-coumaroyl putrescine | Alkaloids | Phenolamine | 3.60 | 2.75 |
pmb0490 | N-p-coumaroyl putrescine | Alkaloids | Phenolamine | 2.68 | 2.44 |
pmb0494 | N-sinapoyl putrescine | Alkaloids | Phenolamine | 2.17 | 1.98 |
pmb0496 | N-feruloyl agmatine | Alkaloids | Phenolamine | 1.15 | 3.72 |
pmb0608 | Chrysoeriol O-malonylhexoside | Flavonoids | Flavonoid | 1.21 | 1.10 |
pmb3081 | Glucarate O-phosphoric acid | Others | Saccharides and alcohols | 1.27 | 1.70 |
pme0008 | L-citrulline | Amino acids and derivatives | Amino acids and derivatives | 1.18 | 1.27 |
pme2596 | 4-Pyridoxic acid | Others | Vitamin | 1.26 | 1.30 |
pme3388 | H-homoArg-OH | Amino acids and derivatives | Amino acids and derivatives | 2.30 | 1.84 |
Rfmb319 | Pipecolic acid | Amino acids and derivatives | Amino acids and derivatives | 1.03 | 1.56 |
Cmyn001733 | 1-Methylpropyl glucosinolate | Others | Glucosinolates | −4.29406 | −3.09 |
CWJP002007 | Kaempferol-3-O-feruloyl-sophoroside-7-oglucoside | Flavonoids | Flavonols | −1.57628 | −1.29 |
Hmbn002228 | kaeperferol-3-O-[2-O-(6-O-E-feruloyl)-β-D-glucopyranosyl]-β-galactopyranoside | Others | Others | −1.14448 | −2.39 |
Lmhn002423 | vnilloylmalic acid | Phenolic acids | Phenolic acids | −4.00812 | −2.29 |
Lnrp102522 | Kaempferol glc-glc-rha | Flavonoids | Flavonols | −3.30626 | −1.23 |
mws1212 | Methyl ferulate | Phenolic acids | Phenolic acids | −1.32806 | −1.24 |
mws1550 | S-allyl-L-cysteine | Amino acids and derivatives | Amino acids and derivatives | −1.65983 | −1.36 |
pmb0382 | O-feruloyl 4-hydroxylcoumarin | Lignans and Coumarins | Coumarins | −2.10723 | −3.09 |
pmb2620 | 3,4-Dimethoxycinnamic acid | Phenolic acids | Phenolic acids | −1.35293 | −1.09 |
pmb3072 | 3-O-p-coumaroyl shikimic acid O-hexoside | Phenolic acids | Phenolic acids | −1.81168 | −2.06 |
pme2914 | 3-Hydroxy-3-methylpentane-1,5-dioic acid | Amino acids and derivatives | Amino acids and derivatives | −1.70006 | −1.99 |
pme3382 | N-acetylthreonine | Amino acids and derivatives | Amino acids and derivatives | −1.98759 | −1.27 |
Zmhn001375 | Vanillic acid-C-glucoside | Phenolic acids | Phenolic acids | −1.91953 | −1.30 |
Zmhn001883 | Vanillic acid glycoside | Phenolic acids | Phenolic acids | −1.64013 | −1.12 |
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Zhang, K.; Yang, D.; Hu, Y.; Njogu, M.K.; Qian, J.; Jia, L.; Yan, C.; Li, Z.; Wang, X.; Wang, L. Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea. Plants 2022, 11, 2229. https://doi.org/10.3390/plants11172229
Zhang K, Yang D, Hu Y, Njogu MK, Qian J, Jia L, Yan C, Li Z, Wang X, Wang L. Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea. Plants. 2022; 11(17):2229. https://doi.org/10.3390/plants11172229
Chicago/Turabian StyleZhang, Kaijing, Dekun Yang, Yuchao Hu, Martin Kagiki Njogu, Jingjing Qian, Li Jia, Congsheng Yan, Ziang Li, Xing Wang, and Liping Wang. 2022. "Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea" Plants 11, no. 17: 2229. https://doi.org/10.3390/plants11172229