Transcriptome Sequencing Reveals Potential Mechanisms of the Maternal Effect on Egg Diapause Induction of Locusta migratoria
Abstract
:1. Introduction
2. Results
2.1. Transcriptomic Analyses
2.2. KEGG Pathways Analysis
2.3. Validations of DEGs Quantitative Real-Time PCR (qRT-PCR)
2.4. Rai1 and foxo Functions Identified by RNAi
2.5. SOD and ROS Activity Changes after RNAi rai1
3. Discussion
3.1. DEGs and Pathways Related to FOXO Signaling Pathway
3.2. Maternal rai1 Regulates Locust Diapause
4. Materials and Methods
4.1. Insect Rearing and Tissue Collection
4.2. RNA Extraction and RNA-Seq
4.3. Sequence Assembly, Annotation and DEGs Analysis
4.4. cDNA Synthesis and qRT-PCR
4.5. RNA Interference
4.6. Diapause Rate Detection
4.7. SOD and ROS Activity Detection
4.8. Statistical Analysis
4.9. Availability of Data and Materials
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
FAT | fat body |
OVA | ovary |
L | long photoperiod |
S | short photperiod |
DEGs | differentially expressed genes |
vs | versus |
FDR | false discovery rate |
BLAST | basic local alignment search tool |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
KO | KEGG Ortholog database |
KOG/COG | Clusters of Orthologous Groups of proteins |
NR | NCBI non-redundant protein sequences |
NT | NCBI nucleotide sequences |
Pfam | protein families |
Swiss-Prot | a manually annotated and reviewed protein sequence database |
TCA cycle | tricarboxylic acid cycle |
fpps | farnesyl diphosphate synthase |
JHamt | juvenile hormone acid O-methyltransferase |
SOD | superoxide dismutase |
PGM | phosphoglucomutase |
GAPDH | glyceraldehyde 3-phosphate dehydrogenase |
ADH | alcohol dehydrogenase |
MDH | malate dehydrogenase |
INSR | insulin receptor |
IRS | insulin receptor substrate |
EGFR | endothelial growth factor receptor |
COX | cytochrome c oxidase |
ND | NADH dehydrogenase |
DR | diapause rate |
foxo | foxo gene |
FOXO | FOXO protein |
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Sample | Clean Reads | Clean Bases (G) | Q20 (%) | Number of Transcripts | Number of Unigenes |
---|---|---|---|---|---|
L_FAT1 | 78872568 | 11.83 | 95.61 | 260,779 | 102,273 |
L_FAT2 | 79227948 | 11.88 | 95.62 | ||
L_FAT3 | 88069778 | 13.21 | 95.86 | ||
S_FAT1 | 77266106 | 11.59 | 96.06 | ||
S_FAT2 | 77647066 | 11.65 | 96.78 | ||
S_FAT3 | 76502530 | 11.48 | 95.71 | ||
L_OVA1 | 80389650 | 12.06 | 95.58 | 323,527 | 132,147 |
L_OVA2 | 90730566 | 13.61 | 95.84 | ||
L_OVA3 | 71022586 | 10.65 | 95.30 | ||
S_OVA1 | 75628016 | 11.34 | 95.92 | ||
S_OVA2 | 88328188 | 13.25 | 96.35 | ||
S_OVA3 | 76316318 | 11.45 | 94.97 |
Group | Num. | Term | ID | p-Value |
---|---|---|---|---|
S_FAT vs. L_FAT up DEGs | 1 | Ribosome | ko03010 | 1.62 × 10−9 |
2 | Citrate cycle (TCA cycle) | ko00020 | 0.003078 | |
3 | Regulation of actin cytoskeleton | ko04810 | 0.012542 | |
4 | Glyoxylate and dicarboxylate metabolism | ko00630 | 0.015929 | |
5 | Glycosphingolipid biosynthesis | ko00603 | 0.019268 | |
6 | Protein processing in endoplasmic reticulum | ko04141 | 0.02064 | |
7 | Endocytosis | ko04144 | 0.021813 | |
8 | Glycolysis / Gluconeogenesis | ko00010 | 0.022633 | |
9 | Cysteine and methionine metabolism | ko00270 | 0.029743 | |
10 | Fc γ R-mediated phagocytosis | ko04666 | 0.029743 | |
S_FAT vs. L_FAT down DEGs | 1 | Glycine, serine and threonine metabolism | ko00260 | 2.21 × 10−5 |
2 | Oxidative phosphorylation | ko00190 | 0.000119 | |
3 | Glyoxylate and dicarboxylate metabolism | ko00630 | 0.000133 | |
4 | Pentose phosphate pathway | ko00030 | 0.000141 | |
5 | Phenylalanine, tyrosine and tryptophan biosynthesis | ko00400 | 0.002921 | |
6 | Fructose and mannose metabolism | ko00051 | 0.006848 | |
7 | Phenylalanine metabolism | ko00360 | 0.013337 | |
8 | Alanine, aspartate and glutamate metabolism | ko00250 | 0.019824 | |
9 | Peroxisome | ko04146 | 0.036338 | |
10 | Arginine biosynthesis | ko00220 | 0.04393 | |
S_OVA vs. L_OVA up DEGs | 1 | Protein processing in endoplasmic reticulum | ko04141 | 3.86 × 10−11 |
2 | Proteasome | ko03050 | 7.15 × 10−7 | |
3 | Spliceosome | ko03040 | 8.36 × 10−5 | |
4 | Cell cycle | ko04110 | 0.000107 | |
5 | Protein export | ko03060 | 0.000334 | |
6 | RNA transport | ko03013 | 0.000422 | |
7 | Antigen processing and presentation | ko04612 | 0.000672 | |
8 | Ubiquitin mediated proteolysis | ko04120 | 0.001973 | |
9 | Pyrimidine metabolism | ko00240 | 0.009155 | |
10 | NOD-like receptor signaling pathway | ko04621 | 0.010726 | |
11 | DNA replication | ko03030 | 0.013664 | |
12 | Toll-like receptor signaling pathway | ko04620 | 0.019418 | |
13 | RNA degradation | ko03018 | 0.021142 | |
14 | Oocyte meiosis | ko04114 | 0.021603 | |
15 | Ribosome | ko03010 | 0.027409 | |
16 | Cytosolic DNA-sensing pathway | ko04623 | 0.033442 | |
17 | Progesterone-mediated oocyte maturation | ko04914 | 0.034639 | |
18 | NF-kappa B signaling pathway | ko04064 | 0.042894 | |
19 | N-Glycan biosynthesis | ko00510 | 0.048725 | |
S_OVA vs. L_OVA down DEGs | 1 | Thyroid hormone signaling pathway | ko04919 | 0.000812 |
2 | Focal adhesion | ko04510 | 0.000986 | |
3 | Hippo signaling pathway - fly | ko04391 | 0.00245 | |
4 | Notch signaling pathway | ko04330 | 0.009375 | |
5 | Tight junction | ko04530 | 0.01335 | |
6 | Dorso-ventral axis formation | ko04320 | 0.018136 | |
7 | Cardiac muscle contraction | ko04260 | 0.021591 | |
8 | ECM-receptor interaction | ko04512 | 0.027292 | |
9 | Longevity regulating pathway | ko04213 | 0.034335 | |
10 | cGMP-PKG signaling pathway | ko04022 | 0.042573 |
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Hao, K.; Jarwar, A.R.; Ullah, H.; Tu, X.; Nong, X.; Zhang, Z. Transcriptome Sequencing Reveals Potential Mechanisms of the Maternal Effect on Egg Diapause Induction of Locusta migratoria. Int. J. Mol. Sci. 2019, 20, 1974. https://doi.org/10.3390/ijms20081974
Hao K, Jarwar AR, Ullah H, Tu X, Nong X, Zhang Z. Transcriptome Sequencing Reveals Potential Mechanisms of the Maternal Effect on Egg Diapause Induction of Locusta migratoria. International Journal of Molecular Sciences. 2019; 20(8):1974. https://doi.org/10.3390/ijms20081974
Chicago/Turabian StyleHao, Kun, Aftab Raza Jarwar, Hidayat Ullah, Xiongbing Tu, Xiangqun Nong, and Zehua Zhang. 2019. "Transcriptome Sequencing Reveals Potential Mechanisms of the Maternal Effect on Egg Diapause Induction of Locusta migratoria" International Journal of Molecular Sciences 20, no. 8: 1974. https://doi.org/10.3390/ijms20081974