Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Growth Conditions
2.2. RNA-Seq
2.3. Reads Alignment, Transcript Assembly and Junction Prediction
2.4. Detection of Alternative Splicing Events
2.5. Identification of Differential Alternative Splicing Events and Differentially Expressed Genes
2.6. Semi-Quantitative RT-PCR Analysis
2.7. Gene Ontology (GO) Analysis and KEGG Analysis
3. Results
3.1. Novel Transcripts and Novel Genes in B. napus
3.2. Identification of AS Events in QY10 and W10 under B Sufficient and Deficient Conditions
3.3. Differential Alternative Splicing in QY10 and W10 in B Deficient Conditions
3.4. DAS Genes and DE Genes in QY10 and W10 in B Deficient Conditions
3.5. SR Splicing Factors in QY10 and W10 under B Deficient Condition
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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No. of Reads (Millions) | Reads Percentage (%) | |
---|---|---|
Starting reads | 2078.8 | - |
Clean reads | 1921.9 | 92.45 |
Mapped reads | 1310.9 | 68.2 |
Sample Name | Novel Transcripts | Reference Like Transcripts | Novel Genes | Reference Like Genes |
---|---|---|---|---|
BsQR1 | 32,762 | 16,656 | 1019 | 5877 |
BsQR2 | 33,451 | 16,384 | 1136 | 5766 |
BsQR3 | 33,662 | 16,661 | 1096 | 5841 |
BsQJL1 | 33,763 | 15,740 | 1147 | 5539 |
BsQJL2 | 35,091 | 15,637 | 1248 | 5742 |
BsQJL3 | 33,274 | 15,608 | 1221 | 5400 |
BsQOL1 | 34,228 | 14,921 | 1288 | 5033 |
BsQOL2 | 34,501 | 14,959 | 1299 | 5074 |
BsQOL3 | 33,610 | 14,592 | 1330 | 4927 |
BdQR1 | 35,565 | 16,441 | 1415 | 5648 |
BdQR2 | 35,780 | 16,570 | 1549 | 5643 |
BdQR3 | 36,428 | 16,731 | 1545 | 5658 |
BdQJL1 | 37,831 | 16,365 | 1601 | 5455 |
BdQJL2 | 36,892 | 16,614 | 1518 | 5625 |
BdQJL3 | 37,677 | 16,124 | 1500 | 5391 |
BdQOL1 | 37,624 | 16,125 | 1685 | 5291 |
BdQOL2 | 35,766 | 16,028 | 1473 | 5339 |
BdQOL3 | 36,421 | 16,189 | 1513 | 5383 |
BsWR1 | 34,561 | 16,128 | 1357 | 5563 |
BsWR2 | 35,245 | 16,801 | 1433 | 5777 |
BsWR3 | 34,940 | 17,124 | 1417 | 5895 |
BsWJL1 | 36,579 | 16,029 | 1513 | 5412 |
BsWJL2 | 38,206 | 16,252 | 1470 | 5382 |
BsWJL3 | 37,242 | 16,214 | 1529 | 5468 |
BsWOL1 | 38,490 | 15,781 | 1812 | 5114 |
BsWOL2 | 37,855 | 15,850 | 1767 | 5161 |
BsWOL3 | 37,224 | 15,411 | 1713 | 5025 |
BdWR1 | 35,174 | 16,653 | 1407 | 5738 |
BdWR2 | 35,790 | 17,013 | 1483 | 5830 |
BdWR3 | 36,108 | 16,838 | 1494 | 5766 |
BdWJL1 | 36,001 | 15,875 | 1498 | 5328 |
BdWJL2 | 37,751 | 16,557 | 1588 | 5538 |
BdWJL3 | 36,854 | 15,976 | 1523 | 5360 |
BdWOL1 | 36,841 | 16,041 | 1559 | 5325 |
BdWOL2 | 36,942 | 15,973 | 1485 | 5335 |
BdWOL3 | 35,714 | 15,746 | 1517 | 5284 |
Cultivars | GeneID | Gene Description | DAS-Type |
---|---|---|---|
QY10 | BnaC09g39180D | alpha/beta-Hydrolases superfamily protein | A5SS |
BnaA06g17710D | alpha-glucan phosphorylase 2 (PHS2) | RI | |
BnaC01g05800D | AME3 | RI | |
BnaC03g31650D | ATOZI1 | A3SS | |
BnaC09g20000D | calcineurin B-like protein 9 (CBL9) | ES | |
BnaC06g30700D | cAMP-regulated phosphoprotein 19-related protein | A3SS | |
BnaC05g02560D | casein kinase like 13 (CKL13) | A5SS | |
BnaC08g08360D | CONSTITUTIVE PHOTOMORPHOGENIC 9 (COP9) | RI | |
BnaA03g27430D | DEAD box RNA helicase family protein | RI | |
BnaA09g27350D | dormancy-associated protein-like 1 (DYL1) | RI | |
BnaA03g39560D | enhancer of ag-4 2 (hua2) | RI | |
BnaC03g57920D | FK506 binding protein 53 (fkbp53) | A3SS | |
BnaAnng37730D | glutathione S-transferase phi 8 (GSTF8) | ES | |
BnaA07g00230D | actin 7 (ACT7) | RI | |
BnaA04g12350D | glycine rich protein 7 (atgrp7) | A5SS | |
BnaC04g04470D | homeodomain GLABROUS 1 (HDG1) | RI | |
BnaA06g30540D | NADH-ubiquinone oxidoreductase B8 subunit, putative | ES | |
BnaA06g38980D | nitrilase 2 (NIT2) | ES | |
BnaC09g20910D | peptide transporter 2 (PTR2) | RI | |
BnaC05g18490D | Phosphoglucomutase/phosphomannomutase family protein | RI | |
BnaA07g16600D | PUR5 | A3SS | |
BnaC05g24350D | radical-induced cell death1 (rcd1) | RI | |
BnaA03g30650D | Ribosomal L29 family protein | ES | |
BnaC09g54460D | Ribosomal protein S13/S18 family | A3SS | |
BnaA07g25750D | RNA-binding (RRM/RBD/RNP motifs) family protein | RI | |
BnaC06g14780D | RSZ32 | A3SS | |
BnaA07g16660D | sedoheptulose-bisphosphatase (SBPASE) | ES | |
BnaC05g08610D | sugar transporter 1 (STP1) | A3SS | |
BnaC04g31660D | TLD-domain containing nucleolar protein | RI | |
BnaA03g07610D | Translation elongation factor EF1B | A3SS | |
BnaC04g56630D | unknown protein | RI | |
BnaCnng63660D | unknown protein | RI | |
BnaC03g03780D | VND-interacting 1 (VNI1) | A3SS | |
W10 | BnaCnng40950D | Cystatin/monellin superfamily protein | A3SS |
BnaC07g51220D | nicotinate phosphoribosyltransferase 1 (NAPRT1) | A5SS |
Tissues | KEGG Pathways | Pathway ID | No. of DAS Gene | p-Value |
---|---|---|---|---|
QR | Spliceosome | ko03040 | 13 | 3.08E-06 |
Carbon metabolism | ko01200 | 7 | 0.034913379 | |
Carbon fixation in photosynthetic organisms | ko00710 | 3 | 0.034913379 | |
Biosynthesis of amino acids | ko01230 | 6 | 0.034913379 | |
mRNA surveillance pathway | ko03015 | 4 | 0.034913379 | |
Glycolysis / Gluconeogenesis | ko00010 | 3 | 0.034913379 | |
Citrate cycle (TCA cycle) | ko00020 | 2 | 0.034913379 | |
Glyoxylate and dicarboxylate metabolism | ko00630 | 2 | 0.034913379 | |
Pyruvate metabolism | ko00620 | 2 | 0.034913379 | |
Sulfur metabolism | ko00920 | 1 | 0.034913379 | |
Nitrogen metabolism | ko00910 | 1 | 0.034913379 | |
Calcium signaling pathway | ko04020 | 1 | 0.034913379 | |
Galactose metabolism | ko00052 | 1 | 0.035225944 | |
MAPK signaling pathway | ko04010 | 1 | 0.035225944 | |
RNA transport | ko03013 | 2 | 0.037548325 | |
Arginine and proline metabolism | ko00330 | 1 | 0.038190214 | |
Starch and sucrose metabolism | ko00500 | 2 | 0.039194028 | |
Amino sugar and nucleotide sugar metabolism | ko00520 | 1 | 0.043604665 | |
Oxidative phosphorylation | ko00190 | 1 | 0.046236768 | |
Plant hormone signal transduction | ko04075 | 2 | 0.047198466 | |
QJL | Carbon fixation in photosynthetic organisms | ko00710 | 4 | 0.011345749 |
Tryptophan metabolism | ko00380 | 3 | 0.011345749 | |
Pentose phosphate pathway | ko00030 | 3 | 0.011345749 | |
Glycolysis / Gluconeogenesis | ko00010 | 3 | 0.019619536 | |
Spliceosome | ko03040 | 4 | 0.019619536 | |
Glyoxylate and dicarboxylate metabolism | ko00630 | 2 | 0.019619536 | |
Pyruvate metabolism | ko00620 | 2 | 0.019619536 | |
ABC transporters | ko02010 | 1 | 0.019619536 | |
Carbon metabolism | ko01200 | 4 | 0.019619536 | |
Fructose and mannose metabolism | ko00051 | 1 | 0.019619536 | |
MAPK signaling pathway | ko04010 | 1 | 0.019619536 | |
Glycine, serine and threonine metabolism | ko00260 | 1 | 0.020680045 | |
Arginine and proline metabolism | ko00330 | 1 | 0.021716355 | |
Starch and sucrose metabolism | ko00500 | 2 | 0.021716355 | |
Peroxisome | ko04146 | 1 | 0.021716355 | |
Pentose and glucuronate interconversions | ko00040 | 1 | 0.021716355 | |
Glutathione metabolism | ko00480 | 1 | 0.021865611 | |
Amino sugar and nucleotide sugar metabolism | ko00520 | 1 | 0.024431115 | |
Plant hormone signal transduction | ko04075 | 2 | 0.026222312 | |
RNA transport | ko03013 | 1 | 0.02673548 | |
Biosynthesis of amino acids | ko01230 | 1 | 0.029409127 | |
QOL | Spliceosome | ko03040 | 7 | 0.030261395 |
AMPK signaling pathway | ko04152 | 5 | 0.030261395 | |
Pyruvate metabolism | ko00620 | 3 | 0.047340426 | |
Tryptophan metabolism | ko00380 | 2 | 0.049084834 | |
WR | Ribosome | ko03010 | 2 | 0.000561484 |
WJL | Peroxisome | ko04146 | 2 | 0.027237847 |
AMPK signaling pathway | ko04152 | 2 | 0.042503393 | |
Glyoxylate and dicarboxylate metabolism | ko00630 | 1 | 0.190757264 | |
Glycolysis / Gluconeogenesis | ko00010 | 1 | 0.278858201 | |
WOL | Starch and sucrose metabolism | ko00500 | 3 | 0.034551184 |
Amino sugar and nucleotide sugar metabolism | ko00520 | 2 | 0.076377304 | |
Pentose phosphate pathway | ko00030 | 1 | 0.165990643 | |
Galactose metabolism | ko00052 | 1 | 0.173014536 |
Sample Names | DAS Genes | DE Genes | Overlap |
---|---|---|---|
BsQR vs. BdQR | 179 | 3404 | 32 |
BsQJL vs. BdQJL | 223 | 1482 | 30 |
BsQOL vs. BdQOL | 178 | 1364 | 8 |
BsWR vs. BdWR | 32 | 2053 | 7 |
BsWJL vs. BdWJL | 47 | 1054 | 1 |
BsWOL vs. BdWOL | 85 | 1181 | 13 |
BsQR vs. BsWR | 174 | 3253 | 10 |
BsQJL vs. BsWJL | 217 | 744 | 4 |
BsQOL vs. BsWOL | 589 | 2769 | 31 |
BdQR vs. BdWR | 37 | 102 | 3 |
BdQJL vs. BdWJL | 49 | 51 | 0 |
BdQOL vs. BdWOL | 62 | 196 | 0 |
Gene Name | Target Genes | Z-Score | Gene Description | DAS Type-Regulation | |||||
---|---|---|---|---|---|---|---|---|---|
Boron Deficient/Boron Sufficient | |||||||||
QR | QJL | QOL | WR | WJL | WOL | ||||
BnaC06g14780D | BnaC04g52770D | 0.92 | Basic-leucine zipper (bZIP) transcription factor | RI | - | - | - | - | - |
BnaC01g37580D | 0.91 | Protein kinase domain | ES | - | ES | ES | - | - | |
BnaA09g52970D | 0.88 | Expansin | RI | - | - | - | - | - | |
BnaA01g14590D | 0.87 | Zinc finger, RING-type | - | - | RI | - | - | - | |
BnaC04g12670D | 0.86 | Folate-biopterin transporter | - | A3SS | - | - | - | - | |
BnaA05g30860D | 0.83 | Glycosyl hydrolase family 100 | - | - | ES | - | - | - | |
BnaC02g31500D | 0.80 | Pectinacetylesterase | - | - | - | - | ES | - | |
BnaA07g32180D | 0.80 | VPS35 homolog B | RI | - | RI | - | - | - | |
BnaA01g30320D | 0.80 | Phosphoglycerate kinase | A3SS | - | - | - | - | - |
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Gu, J.; Li, W.; Wang, S.; Zhang, X.; Coules, A.; Ding, G.; Xu, F.; Ren, J.; Lu, C.; Shi, L. Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes 2019, 10, 224. https://doi.org/10.3390/genes10030224
Gu J, Li W, Wang S, Zhang X, Coules A, Ding G, Xu F, Ren J, Lu C, Shi L. Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes. 2019; 10(3):224. https://doi.org/10.3390/genes10030224
Chicago/Turabian StyleGu, Jin, Wei Li, Sheliang Wang, Xiaoyan Zhang, Anne Coules, Guangda Ding, Fangsen Xu, Jian Ren, Chungui Lu, and Lei Shi. 2019. "Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus" Genes 10, no. 3: 224. https://doi.org/10.3390/genes10030224
APA StyleGu, J., Li, W., Wang, S., Zhang, X., Coules, A., Ding, G., Xu, F., Ren, J., Lu, C., & Shi, L. (2019). Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes, 10(3), 224. https://doi.org/10.3390/genes10030224