Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts
Abstract
:1. Introduction
2. Results
2.1. RNA Sequencing, De Novo Assembly, and Annotations
2.2. Transcriptome Changes in Different Fruit Kernel Stages
2.3. Functional Enrichment Analysis of DEGs
2.4. Overview of the Lipid Composition at Different Fruit Kernel Developmental Stages
2.5. Lipid-Related Gene Expression Changes during Fruit Kernel Development
2.6. Validation of Key Genes Involved in Lipid Regulation Using qRT-PCR Analysis
3. Discussion
3.1. Divergence of Lipid Composition in the Kernels of M. ternifolia
3.2. Lipid Biosynthesis in Fruit Kernels of M. ternifolia
4. Materials and Methods
4.1. Plant Materials, RNA Extraction, and Sequencing
4.2. Transcript Assembly, Annotation, and Analysis of DEGs
4.3. Real-Time qRT-PCR Analysis
4.4. Lipid Extraction and Analysis Using UPLC-MS/MS
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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Sample | Raw Reads | Clean Reads | Clean Base (Gb) | Mapped Reads (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|---|
S1-1 | 55,604,268 | 53,433,146 | 8.0 | 85 | 97.9 | 93.8 | 44.8 |
S1-2 | 56,740,048 | 54,978,858 | 8.3 | 83 | 97.5 | 92.8 | 45.4 |
S1-3 | 50,745,980 | 49,452,818 | 7.4 | 83 | 97.9 | 93.7 | 45.2 |
S2-1 | 49,242,862 | 45,820,088 | 6.8 | 82 | 97.8 | 93.5 | 44.1 |
S2-2 | 46,406,958 | 44,626,700 | 6.7 | 82 | 97.8 | 93.5 | 44.3 |
S2-3 | 48,601,196 | 46,373,882 | 7.0 | 81 | 97.9 | 93.7 | 44.1 |
S3-1 | 55,107,466 | 53,593,048 | 8.0 | 79 | 97.8 | 93.6 | 45.7 |
S3-2 | 46,080,428 | 44,529,822 | 6.7 | 78 | 97.8 | 93.6 | 45.2 |
S3-3 | 56,758,326 | 54,256,348 | 8.1 | 76 | 98.0 | 94.2 | 44.0 |
ID | S1 | S2 | S3 | Annotations |
---|---|---|---|---|
Unigene 73227 | 61.9 | 1.8 | 0.0 | 3-ketoacyl-acyl carrier protein reductase |
Unigene 211387 | 11.5 | 0.2 | 0.0 | 3-ketoacyl-acyl carrier protein reductase |
Unigene 73228 | 10.6 | 0.0 | 0.0 | 3-ketoacyl-acyl carrier protein reductase |
Unigene 163200 | 0.0 | 1.2 | 0.0 | 3-ketoacyl-acyl carrier protein reductase |
Unigene 26385 | 41.6 | 0.0 | 0.0 | 3-ketoacyl-acyl carrier protein reductase |
Unigene 170150 | 108.4 | 640.6 | 3.6 | Beta-glucosidase 11 |
Unigene 41085 | 27.4 | 0.2 | 0.3 | Beta-glucosidase 11 |
Unigene 81638 | 0.3 | 18.4 | 0.0 | Beta-glucosidase 12 |
Unigene 81652 | 1.3 | 22.1 | 0.0 | Beta-glucosidase 12 |
Unigene 91684 | 0.0 | 0.8 | 0.0 | Beta-glucosidase 44 |
Unigene 35002 | 2.6 | 0.1 | 0.0 | Beta-glucosidase 41 |
Unigene 101847 | 0.0 | 0.0 | 1.7 | Choline/ethanolaminephosphotransferase 1 |
Unigene 81642 | 56.3 | 479.2 | 0.1 | Cyanogenic beta-glucosidase |
Unigene 147364 | 0.0 | 5.8 | 2.7 | Diacylglycerol kinase 2 |
Unigene 150581 | 0.0 | 0.7 | 0.0 | Enoyl-acyl-carrier-protein reductase (NADH) |
Unigene 150580 | 0.0 | 1.4 | 0.0 | Enoyl-acyl-carrier-protein reductase (NADH) |
Unigene 140441 | 0.0 | 3.0 | 0.0 | Enoyl-acyl-carrier-protein reductase (NADH) |
Unigene 240247 | 4.6 | 0.0 | 0.1 | GDSL esterase lipase |
Unigene 213504 | 3.7 | 10.1 | 0.0 | GDSL esterase lipase |
Unigene 82774 | 7.5 | 5.7 | 0.0 | GDSL esterase lipase |
Unigene 183098 | 6.6 | 0.9 | 0.0 | GDSL esterase lipase |
Unigene 62756 | 0.0 | 3.2 | 0.1 | GDSL esterase lipase |
Unigene 38911 | 1.4 | 0.0 | 0.0 | GDSL esterase lipase |
Unigene 113245 | 1.4 | 0.0 | 0.0 | GDSL esterase lipase |
Unigene 238268 | 12.8 | 0.5 | 0.0 | GDSL esterase lipase |
Unigene 69671 | 18.5 | 40.2 | 0.5 | GDSL esterase lipase APG |
Unigene 103298 | 5.3 | 11.0 | 0.0 | GDSL esterase lipase APG |
Unigene 152617 | 1.5 | 0.0 | 0.0 | Glycerol-3-phosphate acyltransferase |
Unigene 128368 | 1.1 | 0.0 | 0.0 | Glycerol-3-phosphate acyltransferase |
Unigene 163240 | 1.8 | 1.0 | 0.0 | Hydroxymethylglutaryl-CoA synthase |
Unigene 122230 | 71.4 | 2.0 | 60.9 | Inositol-3-phosphate synthase |
Unigene 9629 | 0.7 | 0.0 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 66716 | 9.1 | 0.1 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 54520 | 1.3 | 0.0 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 59928 | 20.7 | 0.1 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 213589 | 5.5 | 0.0 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 37584 | 19.1 | 0.3 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 34267 | 15.0 | 0.1 | 0.0 | Linoleate 13S-lipoxygenase 2-1 |
Unigene 13471 | 2.4 | 0.1 | 0.0 | Linoleate 9S-lipoxygenase A |
Unigene 5404 | 0.9 | 0.0 | 0.0 | Linoleate 9S-lipoxygenase A |
Unigene 139752 | 0.5 | 0.0 | 0.5 | Lipoxygenase 4 |
Unigene 227869 | 4.6 | 11.8 | 0.1 | Phosphatidylinositol 4-kinase alpha 1 |
Unigene 171746 | 72.5 | 95.5 | 0.6 | Phospholipase A2-alpha |
Unigene 56285 | 0.0 | 0.0 | 0.8 | Phospholipid hydroperoxide |
Unigene 63669 | 24.8 | 20.0 | 0.5 | Pyruvate kinase 2 |
Unigene 63675 | 2.4 | 2.4 | 0.0 | Pyruvate kinase 2 |
Unigene 86831 | 2.8 | 1.0 | 0.0 | Pyruvate kinase 2 |
Unigene 158347 | 4.21 | 0.00 | 0.26 | Non-specific phospholipase C6; EC |
Unigene 190439 | 5.87 | 6.86 | 0.08 | Non-specific phospholipase C2; EC |
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Shi, R.; Bai, H.; Li, B.; Liu, C.; Ying, Z.; Xiong, Z.; Wang, W. Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts. Life 2021, 11, 1431. https://doi.org/10.3390/life11121431
Shi R, Bai H, Li B, Liu C, Ying Z, Xiong Z, Wang W. Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts. Life. 2021; 11(12):1431. https://doi.org/10.3390/life11121431
Chicago/Turabian StyleShi, Rui, Haidong Bai, Biao Li, Can Liu, Zhiping Ying, Zhi Xiong, and Wenlin Wang. 2021. "Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts" Life 11, no. 12: 1431. https://doi.org/10.3390/life11121431
APA StyleShi, R., Bai, H., Li, B., Liu, C., Ying, Z., Xiong, Z., & Wang, W. (2021). Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts. Life, 11(12), 1431. https://doi.org/10.3390/life11121431