Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response
Abstract
:1. Introduction
2. Results and Discussion
2.1. Sequencing and Reads Assembly
Items | Number |
---|---|
Total unigenes | 313,958 |
Max contig length (bp) | 15,986 |
Min contig length (bp) | 205 |
Whole dataset length (bp) | 156,000,000 |
Average contig length (bp) | 497 |
N50 | 572 |
2.2. Annotation of Unigenes
Annotation Database | Number of Annotations | Percent of Annotation (%) |
---|---|---|
Total unigene | 313,958 | - |
Nr | 89,738 | 28.58% |
SWISS-PROT | 61,342 | 19.54% |
TrEMBL | 93,087 | 29.65% |
CDD | 55,710 | 17.74% |
PFAM | 80,756 | 25.72% |
KOG | 43,015 | 13.70% |
Pathway | Id | Number of DEGs with Pathway Annotations (13,204) | Number of Genes with Pathway Annotations (14,105) | p-Value |
---|---|---|---|---|
Metabolism of xenobiotics by cytochrome P450 | ko00980 | 134 (1.02%) | 287 (2.03%) | 3.06 × 10−8 |
Drug metabolism-cytochrome P450 | ko00982 | 122 (0.92%) | 267 (1.89%) | 4.53 × 10−7 |
PPAR signaling pathway | ko03320 | 221 (1.67%) | 548 (3.89%) | 9.40 × 10−7 |
Protein processing in endoplasmic reticulum | ko04141 | 796 (6.03%) | 2332 (16.53%) | 8.32 × 10−6 |
Ribosome biogenesis in eukaryotes | ko03008 | 264 (2.00%) | 705 (5.00%) | 5.85 × 10−5 |
RNA polymerase | ko03020 | 122 (0.92%) | 297 (2.11%) | 1.94 × 10−4 |
Ubiquitin mediated proteolysis | ko04120 | 392 (2.97%) | 1123 (7.06%) | 5.06 × 10−4 |
Proteasome | ko03050 | 313 (2.37%) | 886 (6.28%) | 9.74 × 10−4 |
ABC transporters | ko02010 | 152 (1.15%) | 397 (2.81%) | 9.80 × 10−4 |
Peroxisome | ko04146 | 326 (2.47%) | 929 (6.59%) | 1.11 × 10−3 |
Glutathione metabolism | ko00480 | 248 (1.88%) | 697 (4.94%) | 2.38 × 10−3 |
Alanine, aspartate and glutamate metabolism | ko00250 | 210 (1.59) | 594 (4.21%) | 8.02 × 10−3 |
Pathway | Id | Number of DEGs with Pathway Annotations (13,204) | Number of Genes with Pathway Annotations (14,105) | p-Value |
---|---|---|---|---|
Ribosome | ko03010 | 3988 (30.20%) | 8912 (63.18%) | 8.16 × 10−101 |
Citrate cycle (TCA cycle) | ko00020 | 566 (4.29%) | 1125 (7.98%) | 1.48 × 10−25 |
Regulation of actin cytoskeleton | ko04810 | 584 (4.42%) | 1262 (8.95%) | 3.45 × 10−16 |
Gap junction | ko04540 | 269 (2.04%) | 527 (3.74%) | 1.67 × 10−13 |
Propanoate metabolism | ko00640 | 342 (2.59%) | 722 (5.12%) | 2.32 × 10−11 |
MAPK signaling pathway | ko04010 | 440 (3.33%) | 1016 (7.20%) | 7.54 × 10−8 |
Calcium signaling pathway | ko04020 | 284 (2.15%) | 661 (4.69%) | 5.06 × 10−4 |
d-Glutamine and d-glutamate metabolism | ko00471 | 33 (0.25%) | 58 (0.41%) | 8.42 × 10−4 |
2.3. Validation by Real-Time RT-PCR
Transcript ID | Description | Fold by RNA-Seq | Fold by qPCR |
---|---|---|---|
comp152611_c0_seq1 | Glutathione γ-glutamylcysteinyltransferase | 2.64 | 1.89 |
comp154333_c1_seq2 | Metallothionein-like protein type 2 | 1.90 | 3.68 |
comp100849_c0_seq1 | WRKY transcription factor 22 | 0.44 | 0.62 |
comp123900_c0_seq1 | EREBP-like factor | 1.26 | 1.55 |
comp145580_c0_seq1 | NAC domain-containing protein 90 | 3.58 | 5.22 |
comp160851_c0_seq1 | Metal transporter Nramp2 | 1.29 | 1.43 |
comp142858_c0_seq3 | Nitrate transporter 1.2 | 0.12 | 0.05 |
comp147199_c0_seq1 | Glutathione S-transferase | 6.73 | 8.33 |
comp130772_c0_seq3 | Ethylene-responsive transcription factor ERF071 | 2.89 | 2.47 |
comp1017906_c0_seq1 | Zinc finger CCCH domain-containing protein 40 | 9.86 | 8.73 |
comp162326_c2_seq1 | Myb proto-oncogene protein. plant | 1.27 | 1.38 |
comp423843_c0_seq1 | Transcription factor bHLH104 | 2.41 | 3.04 |
2.4. Analysis of Differential Gene Expression
3. Experimental Section
3.1. Sampling
3.2. cDNA Library Preparation and Sequencing
3.3. Transcriptome Sequencing Results Analysis
3.4. Real-Time RT-PCR
3.5. Analysis of Gene Differential Expression
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Tian, S.; Gu, C.; Liu, L.; Zhu, X.; Zhao, Y.; Huang, S. Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response. Int. J. Mol. Sci. 2015, 16, 28087-28097. https://doi.org/10.3390/ijms161226084
Tian S, Gu C, Liu L, Zhu X, Zhao Y, Huang S. Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response. International Journal of Molecular Sciences. 2015; 16(12):28087-28097. https://doi.org/10.3390/ijms161226084
Chicago/Turabian StyleTian, Songqing, Chunsun Gu, Liangqin Liu, Xudong Zhu, Yanhai Zhao, and Suzhen Huang. 2015. "Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response" International Journal of Molecular Sciences 16, no. 12: 28087-28097. https://doi.org/10.3390/ijms161226084