Main Molecular Pathways Associated with Copper Tolerance Response in Imperata cylindrica by de novo Transcriptome Assembly
Abstract
:1. Introduction
2. Results
2.1. Biomass Production and Localization of Cu in Tissue
2.2. Illumina Sequencing and De novo Transcriptome Assembly
2.3. Multivariate Analysis
2.4. Differential Expression Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Material and Experimental Design
4.2. Cu Localization in Plant Tissues
4.3. RNA-Extraction, Sequencing, and De novo Transcriptome Assembly
4.4. Differential Gene Expression Analysis
4.5. Transcriptome Annotation Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Metric I. cylindrica Transcriptome | |
---|---|
Trinity transcripts | 200,521 |
Trinity “genes” | 113,137 |
GC (%) | 50 |
Contig N50 (bp) | 1918 |
Median contig length (bp) | 978 |
Average contig (bp) | 1377 |
Total assembled bases | 276,047,337 |
Blastx Hit SwissProt | (58%) 117,238 |
Summary of Benchmarking Universal Single-Copy Orthologs (BUSCO) Statistics | ||
---|---|---|
Complete BUSCOs | 1259 | 91.5% |
Complete and single-copy BUSCOs | 560 | 40.7% |
Complete and duplicated BUSCOs | 699 | 50.8% |
Fragmented BUSCOs | 85 | 6.2% |
Missing BUSCOs | 31 | 2.3% |
Total BUSCO genes * | 1375 | 100.0% |
Gene Encoding for | Ontology | FPKM Control | FPKM Treatment | Fold Change (FC) | p-Value |
---|---|---|---|---|---|
Cysteine-rich receptor-like protein kinase 10 | MF: ATP binding (GO:0005524) | 0 | 233.66 | 10.61 | 7.80 × 10−22 |
Protein SULFUR DEFICIENCY-INDUCED 1 | BP: regulation of sulfur utilization (GO:0006792) | 76.03 | 1.06 | −5.11 | 9.00 × 10−5 |
Protein SULFUR DEFICIENCY-INDUCED 1 | BP: cellular response to sulfur starvation (GO:0010438) | 1817.86 | 229.38 | −7.69 | 2.70 × 10−11 |
Phosphate transporter PHO1-3 | PB: phosphate ion transport (GO:0006817) | 98.79 | 11.16 | −4.92 | 1.80 × 10−4 |
Inorganic phosphate transporter 1–11 | BP: phosphate ion transport (GO:0006817) | 2162.05 | 269.6 | −4.69 | 4.30 × 10−4 |
Vacuolar iron transporter homolog 1 | BP: intracellular sequestering of iron ion (GO:0006880) | 44.07 | 0 | −7.57 | 5.70 × 10−11 |
GDP-L-galactose phosphorylase 2 | MF: hydrolase activity (GO:0016787) | 9153.18 | 1541.18 | −6.73 | 1.80 × 10−8 |
Pectin acetylesterase 7 | BP: cell wall organization (GO:0071555) | 211.39 | 13.83 | −4.44 | 1.10 × 10−3 |
Bidirectional sugar transporter SWEET3a | MF: sugar transmembrane transporter activity (GO:0051119) | 104.55 | 3.94 | −4.58 | 6.40 × 10−4 |
RNA exonuclease 4 | PB: rRNA processing (GO:0006364) | 53.93 | 5.02 | −4.65 | 4.9 × 10−4 |
Gene Encoding for | Ontology | FPKM Control | FPKM Treatment | Fold Change (FC) | p-Value |
---|---|---|---|---|---|
Superoxide dismutase [Mn], mitochondrial | PB: removal of superoxide radicals (GO:0019430) | 94.74 | 0 | −4.08 | 6.79 × 10−4 |
Extracellular superoxide dismutase [Cu-Zn] | PB: removal of superoxide radicals (GO:0019430) | 77.17 | 0 | −3.82 | 1.62 × 10−3 |
Superoxide dismutase [Cu-Zn] | PB: removal of superoxide radicals (GO:0019430) | 0.55 | 25.13 | 3.90 | 1.3 x10−3 |
Superoxide dismutase [Cu-Zn] 2 | PB: removal of superoxide radicals (GO:0019430) | 6.68 | 82.63 | 4.36 | 2.5 × 10−4 |
Superoxide dismutase [Fe] | MF: superoxide dismutase activity (GO:0004784) | 12.32 | 82.56 | 4.17 | 5.0 × 10−4 |
Copper transport protein ATOX1 | BP: cellular copper ion homeostasis (GO:0006878) | 47.45 | 0 | −3.53 | 4.07 × 10−3 |
Hephaestin-like protein | BP:copper ion transport (GO:0006825) | 2.68 | 36.63 | 5.17 | 9.6 × 10−6 |
Probable copper-transporting ATPase HMA5 | BP:detoxification of copper ion (GO:0010273) | 1.72 | 23.09 | 3.95 | 1.1 × 10−3 |
Protein NBR1 homolog | BP:protein transport (GO:0015031) | 9.18 | 100.88 | 7.02 | 5.0 × 10−10 |
ABC transporter C family member 8 | BP: transmembrane transport (GO:0055085) | 5.41 | 34.58 | 3.88 | 1.3 × 10−3 |
Actin, muscle | CC: cytoskeleton (GO:0005856) | 92.68 | 3.17 | −4.37 | 2.34 × 10−4 |
Actin | CC: cytoskeleton (GO:0005856) | 7459.58 | 1584.51 | −4.14 | 5.38 × 10−4 |
Actin-1 | CC: cytoskeleton (GO:0005856) | 162.63 | 18.93 | −3.80 | 1.72 × 10−3 |
Actin-87E | CC: cytoskeleton (GO:0005856) | 1441.51 | 0.49 | −6.70 | 3.39 × 10−9 |
Actin-1 | CC: cytoskeleton (GO:0005856) | 13.44 | 218.38 | 4.98 | 2.2 × 10−5 |
Actin-related protein 2 | MF:actin binding (GO:0003779) | 0.55 | 46.29 | 6.28 | 4.0 × 10−8 |
Actobindin-A | MF:actin binding (GO:0003779) | 5.49 | 234.97 | 6.19 | 6.6 × 10−8 |
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Vidal, C.; Larama, G.; Riveros, A.; Meneses, C.; Cornejo, P. Main Molecular Pathways Associated with Copper Tolerance Response in Imperata cylindrica by de novo Transcriptome Assembly. Plants 2021, 10, 357. https://doi.org/10.3390/plants10020357
Vidal C, Larama G, Riveros A, Meneses C, Cornejo P. Main Molecular Pathways Associated with Copper Tolerance Response in Imperata cylindrica by de novo Transcriptome Assembly. Plants. 2021; 10(2):357. https://doi.org/10.3390/plants10020357
Chicago/Turabian StyleVidal, Catalina, Giovanni Larama, Aníbal Riveros, Claudio Meneses, and Pablo Cornejo. 2021. "Main Molecular Pathways Associated with Copper Tolerance Response in Imperata cylindrica by de novo Transcriptome Assembly" Plants 10, no. 2: 357. https://doi.org/10.3390/plants10020357