De Novo Transcriptome Sequencing in Passiflora edulis Sims to Identify Genes and Signaling Pathways Involved in Cold Tolerance
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Total RNA Extraction, cDNA Library Preparation and Transcriptome Sequencing
2.3. Transcriptome Assembly and Function Annotation
2.4. Differential Expression Analysis
2.5. Quantitative Real-Time PCR (qRT-PCR)
3. Results
3.1. Transcriptome Sequencing and De Novo Assembly
3.2. Function Annotation and Classification
3.3. DEG Identification, GO and KEGG Enrichment Analysis
3.4. DEGs Involved in the Plant Hormone Signal Transduction Pathways
3.5. Verification by qRT-PCR
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
Nr | NCBI non-redundant protein sequences |
Nt | NCBI non-redundant nucleotide sequences |
Pfam | Protein family |
COG | Clusters of orthologous groups of proteins |
KOG | EuKaryotic Orthologous Groups |
Swiss-Prot | A manually annotated and reviewed protein sequence database |
KEGG | Kyoto encyclopedia of genes and genomes |
KO | KEGG ortholog database |
GO | Gene ontology |
FPKM | Fragments per kilobase of exon per million fragments mapped |
DEGs | Differentially expressed genes |
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Nucleotide Length | Transcripts | Unigenes |
---|---|---|
200–500 bp | 60,598 | 20,947 |
0.5–1k bp | 22,605 | 21,684 |
1–2k bp | 22,073 | 22,051 |
>2k bp | 22,198 | 22,198 |
Total | 127,474 | 86,880 |
Min length (bp) | 201 | 201 |
Mean length (bp) | 1077 | 1449 |
Max length (bp) | 13,397 | 13,397 |
N50 (bp) | 2057 | 2222 |
Component | Number of Unigenes | Percentage (%) |
---|---|---|
Annotated in NCBI non-redundant protein sequences (NR) | 60,028 | 69.09 |
Annotated in NCBI non-redundant nucleotide sequences (NT) | 46,093 | 53.05 |
Annotated in KEGG ortholog database (KO) | 24,312 | 27.98 |
Annotated in Swiss-Prot | 47,717 | 54.92 |
Annotated in Pfam | 45,544 | 52.42 |
Annotated in Gene ontology (GO) | 46,754 | 53.81 |
Annotated in EuKaryotic Orthologous Groups (KOG) | 17,742 | 20.42 |
Annotated in all databases | 10,457 | 12.03 |
Annotated in at least one database | 64,067 | 73.74 |
Total unigenes | 86,880 |
Component | Unigenes | DEGs | Ratio (%) |
---|---|---|---|
AP2/EREBP | 216 | 8 | 3.7 |
WRKY | 161 | 12 | 7.5 |
bZIP | 181 | 8 | 4.4 |
MYB | 387 | 14 | 3.6 |
NAC | 221 | 11 | 5.0 |
B-ARR | 20 | 3 | 15 |
CaM/CBLs | 332 | 14 | 4.2 |
MAPK | 93 | 11 | 11.8 |
LEA | 38 | 4 | 10.5 |
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Liu, S.; Li, A.; Chen, C.; Cai, G.; Zhang, L.; Guo, C.; Xu, M. De Novo Transcriptome Sequencing in Passiflora edulis Sims to Identify Genes and Signaling Pathways Involved in Cold Tolerance. Forests 2017, 8, 435. https://doi.org/10.3390/f8110435
Liu S, Li A, Chen C, Cai G, Zhang L, Guo C, Xu M. De Novo Transcriptome Sequencing in Passiflora edulis Sims to Identify Genes and Signaling Pathways Involved in Cold Tolerance. Forests. 2017; 8(11):435. https://doi.org/10.3390/f8110435
Chicago/Turabian StyleLiu, Sian, Anding Li, Caihui Chen, Guojun Cai, Limin Zhang, Chunyan Guo, and Meng Xu. 2017. "De Novo Transcriptome Sequencing in Passiflora edulis Sims to Identify Genes and Signaling Pathways Involved in Cold Tolerance" Forests 8, no. 11: 435. https://doi.org/10.3390/f8110435