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| Status |
Public on May 26, 2021 |
| Title |
Differential transcriptome analysis reveals genes related to low- and high-temperature stress in the fall armyworm (Spodoptera frugiperda) |
| Organism |
Spodoptera frugiperda |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: We aimed to use RNA-Seq and de novo transcriptome assembly to produce transcriptomes and analyze the changes in transcription regulation associated with cold and heat treatment in Spodoptera frugiperda. A detailed differential expression analysis revealed a number of candidate genes that may be associated with FAW cold and heat tolerance. To validate the RNA-seq results, we used qRT-PCR. We hoped to provide a foundation for the adaptive mechanism as well as a rich resource for the discovery and detection of novel genes involved in cold and heat stress responses of Spodoptera frugiperda.
Methods: Spodoptera frugiperda was reared at lab condition, and incubated at 2 different temperature( 4 and 40°C) for 16 hours as temperature treatment groups. RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions.
Results: A total of 211,967 unigenes were collected, at least 14,338 of which were annotated with gene descriptions, gene ontology terms, and metabolic pathways. There were 50 GO functional sub-groups and 21 EggNOG words as a result. DEGs with log2FC≥2 were identified and compared at various temperatures. In comparison to the 25°C treated group, we discovered 199 and 1248 individual DEGs co-regulated at 4 and 40°C, respectively. Comparing transcriptome profiles for differential gene expression revealed a number of DE genes, including cytochrome P450, odorant binding proteins (OBP), and immune system genes previously implicated in cold and high temperature resistance. The enrichment pathways were identified using KEGG analysis, and heatmaps of similar unigenes from both treatment groups (T4 and T40) were plotted. We used qPCR to confirm the RNA-seq data on 10 up- and down-regulated DEGs.
Conclusions: In conclusion, we used RNA-Seq technology focused on high-throughput sequencing to compare the transcriptomes of Spodoptera frugiperda under high- and low-temperature stresses. This research was the first to identify a large number of genes that were significantly up-regulated at high and low temperatures. Many genes were discovered through comparative transcriptome analysis, and a significant number of improvements in metabolic pathways were discovered through GO and KEGG enrichment analysis. Our findings will help future molecular research and genomic studies. These newly found genes may be important and necessary to FAW harsh environment tolerance and its behavior for adaptation in new environment as well as quarantine area.
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| Overall design |
Total RNA of Spodoptera frugiperda for two different treated temperatures was extracted. The control group consisted of larvae incubated at 25°C
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| Contributor(s) |
Vatanparast M, Park Y |
| Citation(s) |
35173626 |
| Submission date |
May 25, 2021 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Mohammad Vatanparast |
| E-mail(s) |
mdvatanparast@gmail.com
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| Organization name |
Animal and Plant Quarantine Agency
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| Department |
Plant quarantine technology center
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| Street address |
167, Yongjeon-ro
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| City |
Gimcheon |
| ZIP/Postal code |
39660 |
| Country |
South Korea |
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| Platforms (1) |
| GPL29193 |
Illumina NovaSeq 6000 (Spodoptera frugiperda) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA732697 |
| SRA |
SRP321312 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE175545_data3_FAW-40_vs_FAW-25_fc2_raw.p.xlsx |
4.5 Mb |
(ftp)(http) |
XLSX |
| GSE175545_data3_FAW-40_vs_FAW-4_fc2_raw.p.xlsx |
4.1 Mb |
(ftp)(http) |
XLSX |
| GSE175545_data3_FAW-4_vs_FAW-25_fc2_raw.p.xlsx |
2.5 Mb |
(ftp)(http) |
XLSX |
| GSE175545_merge_Trinity_Unigene.fasta.gz |
51.7 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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