Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Insects
2.2. RNA Isolation
2.3. Large RNA Library Construction and Sequencing
2.4. Small RNA Library Construction and Sequencing
2.5. Synthesis of cDNA
2.6. qRT-PCR Amplification of Spinosad-Associated Transcripts Identified via NGS
2.7. Functional Assessment of Spinosad-Modulated mRNAs
3. Results
3.1. mRNA Expression in Spinosad-Exposed L. decemlineata by NGS
3.2. qRT-PCR-Based Expression of Transcripts Modulated by Spinosad in L. decemlineata as Determined by NGS
3.3. miRNA Expression in Control and Spinosad-Exposed Insects via NGS
3.4. Functional Classification of Differentially Expressed mRNA Transcripts Following Spinosad Treatment
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Primer | Sequence | Efficiency | Temperature | |
---|---|---|---|---|
Cathepsin B | Fwd Rev | 5′-TTCGATGCACGAGAAAATTG-3′ | 100.3% | 57.7 °C |
5′-CTCATGACGGAAGTTGCTGA-3′ | ||||
Cathepsin L-like proteinase | Fwd Rev | 5′-AACGCAGTAGGTACCGTTGG-3′ | 101.3% | 57.1 °C |
5′-CAGCCAAAACACCATGATTG-3′ | ||||
Lysosomal alpha-mannosidase | Fwd Rev | 5′-GAAATTGGTTCAGCCTTGGA-3′ | 99.8% | 58.1 °C |
5′-ATAGCTGCGCGTCTTCATTT-3′ | ||||
Multidrug resistance-associated protein 4 | Fwd Rev | 5′-TCCAATGTGCGAAACAACAT-3′ | 102.1% | 57.1 °C |
5′-GGCAAAGGGAAATTGTTTGA-3′ | ||||
Senecionine N-oxygenase | Fwd Rev | 5′-TGTTGTGGTTTCGACGTCAT-3′ | 103.6% | 58.1 °C |
5′-TACGTTGAACGGAACACCAA-3′ | ||||
Voltage-dependent calcium channel type A subunit alpha-1 | Fwd Rev | 5′-AGCATAGCCATCCATCCTTG-3′ | 100.4% | 63.2 °C |
5′-GAGTCTGCGGTGTAGCATGA-3′ | ||||
α-tubulin | Fwd Rev | 5′-GAGTTCCAGACCAACTTGGT-3′ | 107.9% | 52.6 °C |
5′-GCCATGTACTTGCCGTGACG-3′ |
Target Accession Number | Target Name | Log2 Fold-Change | p-Value |
---|---|---|---|
Spinosad/Control | |||
LOC111514273 | Peritrophin-1-like | 2.08 | 0.046 |
LOC111505285 | Polygalacturonase-like|glycoside hydrolase family 28 | 1.88 | 0.020 |
LOC111505933 | Cathepsin B-like | 1.83 | 0.019 |
LOC111509352 | Lysosomal alpha-mannosidase-like | 1.65 | 0.003 |
LOC111507304 | Venom carboxylesterase-6-like | 1.60 | 0.036 |
LOC111501823 | Lysosomal alpha-mannosidase-like | 1.45 | 0.041 |
LOC111512755 | Cathepsin L-like proteinase | 1.45 | 0.039 |
LOC111513337 | GILT-like protein 1 | 1.43 | 0.023 |
LOC111517731 | Uncharacterized protein LOC111517731 | 1.39 | 0.032 |
LOC111513667 | Tetratricopeptide repeat protein 39B-like | 1.38 | 0.016 |
LOC111512533 | Probable chitinase 10 | 1.30 | 0.048 |
LOC111510455 | Equilibrative nucleoside transporter 3-like | 1.28 | 0.041 |
LOC111511653 | Uncharacterized protein LOC111511653 | 1.24 | 0.012 |
LOC111512328 | Juvenile hormone esterase-like | 1.23 | 0.024 |
LOC111513728 | Cathepsin L-like proteinase | 1.20 | 0.006 |
LOC111503028 | Neutral alpha-glucosidase C-like | 1.16 | 0.028 |
LOC111512041 | Venom carboxylesterase-6-like | 1.16 | 0.008 |
LOC111505338 | Uncharacterized protein LOC111505338 | 1.13 | 0.035 |
LOC111503007 | Multidrug resistance-associated protein 4-like | 1.02 | 0.007 |
LOC111513768 | Juvenile hormone acid O-methyltransferase-like | 1.02 | 0.044 |
LOC111507306 | Venom carboxylesterase-6-like | 1.01 | 0.006 |
LOC111504230 | Uncharacterized protein LOC111504230 | −1.04 | 0.001 |
LOC111516463 | Probable cytochrome P450 301a1, mitochondrial|cytochrome P450 12h2 | −1.07 | 0.008 |
LOC111507554 | Uncharacterized protein LOC111507554 | −1.10 | 0.033 |
LOC111512100 | Neuropeptide-like protein 31 | −1.20 | 0.050 |
LOC111513879 | Lipase 3-like | −1.32 | 0.020 |
LOC111507616 | Senecionine N-oxygenase-like | −1.86 | 0.025 |
LOC111517073 | Putative nuclease HARBI1 | −2.24 | 0.020 |
LOC111507833 | Voltage-dependent calcium channel type A subunit alpha-1-like | −2.83 | 0.033 |
LOC111513727 | Cathepsin L-like proteinase | −5.13 | 0.005 |
Target Accession Number | Target Name | Log2 Fold-Change | p-Value |
---|---|---|---|
Spinosad/Control | |||
LOC111506250 | Cytochrome P450 9e2-like | 1.41 | 0.051 |
LOC111510879 | Cytochrome P450 6k1-like | 0.92 | 0.069 |
LOC111517755 | Probable cytochrome P450 6a23/cytochrome P450 | 0.91 | 0.026 |
LOC111517753 | Probable cytochrome P450 6a23/cytochrome P450 6bj3 | 0.57 | 0.064 |
LOC111503064 | Cytochrome P450 4g15 | 0.42 | 0.071 |
LOC111505596 | Endocuticle structural glycoprotein SgAbd-4-like/putative cuticle protein CP6 | 0.39 | 0.067 |
LOC111505534 | NADPH-cytochrome P450 reductase | 0.33 | 0.041 |
LOC111503441 | Cytochrome P450 4c1-like | 0.31 | 0.022 |
LOC111517496 | Endocuticle structural glycoprotein SgAbd-8-like | −0.30 | 0.095 |
LOC111505902 | Cytochrome P450 CYP12a2-like/cytochrome P450 353a2 | −0.49 | 0.059 |
LOC111509981 | Cytochrome P450 4c1-like | −1.06 | 0.076 |
LOC111516463 | Probable cytochrome P450 301a1, mitochondrial/cytochrome P450 12h2 | −1.07 | 0.008 |
miRNAs | Average Normalized Expression |
---|---|
Lde-miR-8-3p | 65,301.25 |
Lde-miR-14-5p | 63,662.96 |
Lde-miR-317-5p | 42,146.90 |
Lde-miR-1-3p | 24,099.48 |
Lde-bantam-3p | 14,830.90 |
Lde-miR-281-5p | 12,820.94 |
Lde-miR-1175-3p | 9564.56 |
Lde-miR-34-3p | 8436.31 |
Lde-miR-12-3p | 6915.56 |
Lde-miR-13b-3p | 6217.84 |
miRNAs | Log2 Fold-Change | p-Value |
---|---|---|
Spinosad/Control | ||
Lde-miR-750-3p | 1.72 | 0.0034 |
Lde-miR-2796-5p | 1.68 | 0.0190 |
Lde-miR-3791-5p | 1.50 | 0.0333 |
Lde-miR-750-5p | 1.07 | 0.0003 |
Lde-bantam-5p | 0.99 | 0.0399 |
Lde-miR-1175-3p | 0.92 | 0.0087 |
Lde-miR-184-3p | 0.87 | 0.0045 |
Lde-miR-281-5p | 0.67 | 0.0296 |
Lde-miR-125-3p | 0.64 | 0.0263 |
Lde-miR-9e-3-5p | −0.69 | 0.0071 |
Lde-let-7-3p | −0.76 | 0.0267 |
Lde-miR-8-3p | −0.76 | 0.0109 |
Lde-miR-9a-5p | −0.97 | 0.0001 |
Lde-miR-12-3p | −1.01 | 0.0057 |
Target Accession Number | Target Name | GO IDs | GO Terms |
---|---|---|---|
LOC111501823 | Lysosomal alpha-mannosidase | P:GO:0044238; P:GO:0071704 | P:primary metabolic process; P:organic substance metabolic process |
LOC111512533 | Uncharacterized protein LOC101463243 isoform X2 | P:GO:0006508; P:GO:0006897 | P:proteolysis; P:endocytosis |
LOC111510455 | Equilibrative nucleoside transporter 1 | P:GO:1901642 | P:nucleoside transmembrane transport |
LOC111503007 | Probable multidrug resistance-associated protein lethal(2)03659 | P:GO:0001666; P:GO:0006979; P:GO:0008340; P:GO:0034059; P:GO:0048190 | P:response to hypoxia; P:response to oxidative stress; P:determination of adult lifespan; P:response to anoxia; P:wing disc dorsal/ventral pattern formation |
LOC111516463 | Probable cytochrome P450 301a1, mitochondrial | P:GO:0055114; P:GO:0007490 | P:oxidation-reduction process; P:tergite morphogenesis |
LOC111513879 | Lipase 1 | P:GO:0006629; P:GO:0016042 | P:lipid metabolic process; P:lipid catabolic process |
LOC111507833 | Voltage-dependent calcium channel type A subunit alpha-1 isoform X14 | P:GO:0006811 | P:ion transport |
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Bastarache, P.; Wajnberg, G.; Dumas, P.; Chacko, S.; Lacroix, J.; Crapoulet, N.; Moffat, C.E.; Morin, P., Jr. Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata. Insects 2020, 11, 820. https://doi.org/10.3390/insects11110820
Bastarache P, Wajnberg G, Dumas P, Chacko S, Lacroix J, Crapoulet N, Moffat CE, Morin P Jr. Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata. Insects. 2020; 11(11):820. https://doi.org/10.3390/insects11110820
Chicago/Turabian StyleBastarache, Pierre, Gabriel Wajnberg, Pascal Dumas, Simi Chacko, Jacynthe Lacroix, Nicolas Crapoulet, Chandra E. Moffat, and Pier Morin, Jr. 2020. "Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata" Insects 11, no. 11: 820. https://doi.org/10.3390/insects11110820