Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Growth under Acidic Soil Conditions
2.2. Contents of Photosynthetic Pigments and Pn-PAR Response Curves
2.3. RNA Isolation and Iron Walnut RNA-Seq
2.4. DEG Identification and Functional Annotation
2.5. Acid-Responsive Gene Identification and Enrichment Analysis
2.6. Quantitative Real-Time PCR (qRT-PCR) Validation
3. Results
3.1. Determination of Pn-PAR Response Curves and Photosynthetic Pigment Contents
3.2. Illumina Sequencing of Different cDNA Libraries
3.3. DEG Analysis and Validation of the Iron Walnut Sequencing Data
3.4. GO-and KEGG-Annotated DEGs
3.5. STEM Cluster Analysis of DEGs and Identification of Acid Resistance-Related Genes
3.6. Molecular Phylogenetic Analysis of Acid Resistance-Related Genes
3.7. Gene Function and Pathway Enrichment Analyses of Acid Resistance-Related Genes
4. Discussion
4.1. Acid Resistance-Related Gene Identification
4.2. Analysis of Acid Resistance-Related Genes
4.3. Hypothetical Regulatory Mechanisms of Acid Resistance
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | Clean Reads | Q30 | GC | Mapped Genome | Unique Mapped Genome | Mapped Genes | Expressed Genes |
---|---|---|---|---|---|---|---|
pH 3–4_1 | 28,020,622 | 94.93% | 45.98% | 87.60% | 68.87% | 75.69% | 26,186 |
pH 3–4_2 | 26,738,560 | 96.36% | 46.37% | 82.25% | 63.00% | 69.82% | 28,134 |
pH 3–4_3 | 27,011,236 | 96.32% | 46.85% | 85.60% | 66.22% | 73.12% | 28,922 |
pH 4–5_1 | 27,605,126 | 96.02% | 46.39% | 85.75% | 68.97% | 74.31% | 27,392 |
pH 4–5_2 | 27,634,854 | 96.44% | 47.05% | 88.56% | 70.73% | 75.93% | 27,670 |
pH 4–5_3 | 27,109,750 | 96.50% | 46.59% | 87.53% | 69.72% | 75.85% | 27,582 |
pH 5–6_1 | 26,864,464 | 96.47% | 46.51% | 87.59% | 71.06% | 73.90% | 26,644 |
pH 5–6_2 | 27,448,384 | 96.36% | 46.37% | 84.86% | 67.01% | 73.6% | 27,525 |
pH 5–6_3 | 27,338,826 | 96.40% | 46.60% | 87.13% | 68.69% | 75.66% | 26,942 |
pH 6–7_1 | 27,698,734 | 94.98% | 46.42% | 88.08% | 68.34% | 76.53% | 26,864 |
pH 6–7_2 | 27,894,576 | 96.50% | 46.45% | 84.43% | 66.27% | 72.39% | 27,221 |
pH 6–7_3 | 27,288,782 | 96.36% | 46.73% | 86.17% | 69.15% | 72.39% | 26,706 |
Gene ID | Forward Primer (5′ to 3′) | Reverse Primer (5′ to 3′) | Amplicon Size (bp) |
---|---|---|---|
gene17916 | GAAGGCGAAGAAGAAGAAGA | CTGGCGGTAACTGTAACTC | 96 |
gene22045 | GGCGTGAAGGAGTTGATT | ACAGTGTTAAGGTCGTATCG | 97 |
gene25150 | AAGACGATGTTGATGATTCC | TTCCAGTATTAGCGGTAAGA | 100 |
gene25184 | TGAGGCTGAAGAGTATGC | CGTAGATGGTTGGATGGT | 82 |
gene29464 | CTGTGTTGTGGTAGAGGA | TCTTCATCGGCTGTGTAA | 81 |
gene29846 | GAGAAGGCTATCACAAGAAG | CCAGTATGACAAGGAGTAATC | 113 |
gene31088 | GATGCTGTGTTGCTGTTC | CCGCCATTATCTGCTTGA | 131 |
gene31799 | GCTATAACTACGCTATATTCG | TTACTTCTGATTCTCCTATGT | 111 |
gene35192 | GCTGGAAGTCATAGTAAGG | ATGGCTGCTAATCACAAG | 167 |
gene39645 | GAGTGGGAATGAAGGAAGA | ATTGGCAGAGGAATTGGA | 72 |
Pathway ID | Pathway | FDR < 0.05 | No. DEGs |
---|---|---|---|
ko01200 | Carbon metabolism | 5.70 × 10−7 | 50 |
ko01100 | Metabolic pathways | 5.70 × 10−7 | 229 |
ko01110 | Biosynthesis of secondary metabolites | 1.65 × 10−6 | 146 |
ko00710 | Carbon fixation in photosynthetic organisms | 1.83 × 10−6 | 28 |
ko00630 | Glyoxylate and dicarboxylate metabolism | 8.98 × 10−6 | 17 |
ko00908 | Zeatin biosynthesis | 2.25 × 10−5 | 14 |
ko00195 | Photosynthesis | 1.20 × 10−4 | 12 |
ko00010 | Glycolysis/gluconeogenesis | 1.04 × 10−3 | 29 |
ko03430 | Mismatch repair | 1.81 × 10−3 | 2 |
ko03050 | Proteasome | 1.81 × 10−3 | 1 |
ko00220 | Arginine biosynthesis | 2.13 × 10−3 | 10 |
ko00903 | Limonene and pinene degradation | 4.64 × 10−3 | 14 |
ko00910 | Nitrogen metabolism | 4.64 × 10−3 | 10 |
ko00030 | Pentose phosphate pathway | 4.64 × 10−3 | 20 |
ko01230 | Biosynthesis of amino acids | 5.00 × 10−3 | 35 |
ko00071 | Fatty acid degradation | 5.88 × 10−3 | 6 |
ko00511 | Other glycan degradation | 6.71 × 10−3 | 1 |
ko00500 | Starch and sucrose metabolism | 7.97 × 10−3 | 40 |
ko00670 | One carbon pool by folate | 8.93 × 10−3 | 7 |
ko04075 | Plant hormone signal transduction | 1.07 × 10−2 | 43 |
ko00260 | Glycine, serine and threonine metabolism | 1.22 × 10−2 | 13 |
ko00250 | Alanine, aspartate and glutamate metabolism | 1.42 × 10−2 | 9 |
Ko00330 | Arginine and proline metabolism | 1.42 × 10−2 | 7 |
ko00051 | Fructose and mannose metabolism | 1.42 × 10−2 | 17 |
ko03015 | mRNA surveillance pathway | 1.60 × 10−2 | 1 |
ko03040 | Spliceosome | 1.60 × 10−2 | 2 |
ko01040 | Biosynthesis of unsaturated fatty acids | 2.06 × 10−2 | 1 |
ko00945 | Stilbenoid, diarylheptanoid and gingerol biosynthesis | 2.06 × 10−2 | 4 |
ko00450 | Selenocompound metabolism | 2.15 × 10−2 | 7 |
ko00740 | Riboflavin metabolism | 2.25 × 10−2 | 4 |
ko04626 | Plant-pathogen interaction | 2.72 × 10−2 | 51 |
ko00052 | Galactose metabolism | 2.90 × 10−2 | 12 |
ko00943 | Isoflavonoid biosynthesis | 2.90 × 10−2 | 1 |
ko00240 | Pyrimidine metabolism | 2.90 × 10−2 | 2 |
ko00592 | α-linolenic acid metabolism | 3.33 × 10−2 | 6 |
ko00196 | Photosynthesis-antenna proteins | 4.07 × 10−2 | 4 |
ko00942 | Anthocyanin biosynthesis | 4.44 × 10−2 | 6 |
ko04141 | Protein processing in endoplasmic reticulum | 4.44 × 10−2 | 40 |
Gene ID | Descriptions | |
---|---|---|
GO Terms | KEGG Pathways | |
gene42780 | spermidine hydroxycinnamoyl transferase-like | |
---- | ko01110, Biosynthesis of secondary metabolites | |
ko01100, Metabolic pathways | ||
ko00945, Stilbenoid, diarylheptanoid and gingerol biosynthesis | ||
ko00941, Flavonoid biosynthesis | ||
ko00940, Phenylpropanoid biosynthesis | ||
gene28192 | spermine synthase-like | |
GO:0003674, molecular function GO:0003824, catalytic activity | ko00410, β-Alanine metabolism | |
ko00480, Glutathione metabolism | ||
ko00270, Cysteine and methionine metabolism | ||
ko00330, Arginine and proline metabolism | ||
ko01100, Metabolic pathways | ||
gene4089 | S-adenosylmethionine synthase 1-like | |
---- | ko01230, Biosynthesis of amino acids | |
gene31260 | arginine decarboxylase-like | |
---- | ko00330, Arginine and proline metabolism | |
gene24987 | serine/arginine-rich splicing factor RS40-like | |
---- | ko03040, Spliceosome | |
gene9388 | mitochondrial arginine transporter BAC2-like | |
GO:0016053, organic acid biosynthetic process | ko04714, Thermogenesis | |
GO:0046394, carboxylic acid biosynthetic process | ||
GO:0005488, binding | ||
GO:0006810, transport |
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Luo, X.; Liu, J. Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut. Genes 2019, 10, 605. https://doi.org/10.3390/genes10080605
Luo X, Liu J. Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut. Genes. 2019; 10(8):605. https://doi.org/10.3390/genes10080605
Chicago/Turabian StyleLuo, Xiaomei, and Juncheng Liu. 2019. "Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut" Genes 10, no. 8: 605. https://doi.org/10.3390/genes10080605
APA StyleLuo, X., & Liu, J. (2019). Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut. Genes, 10(8), 605. https://doi.org/10.3390/genes10080605