Dataset Information

Comparative transcriptome analysis of Solenopsis japonica (Hymenoptera: Formicidae) under low temperature and normal room temperature

ABSTRACT: Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold stress response in Solenopsis japonica. Retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Solenopsis japonica was reared at lab condition, and incubated at 2 different temperature for 24h (9, and 25℃) under dark conditions. 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: Totally 89,657 unigenes was obtained which overall 43,375 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 25 EggNOG terms resulted. DEGs with FC≥2 and FC≤-2, P-value<0.05 were screened and were compared at two different temperatures. We found 138 DEG down regulated and 271 DEG up regulated when the S. japonica incubated at 9 ℃ and compared with 25℃ treated group. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress. Conclusions: we compared the transcriptomes of S. japonica under normal room temperature and low-temperature using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to S. japonica overwintering and its behavior for adaptation in new environment.

ORGANISM(S): Solenopsis japonica

PROVIDER: GSE155469 | GEO | 2020/08/01

REPOSITORIES: GEO

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Project description:Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold and heat stress response in Solenopsis invicta. retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Solenopsis invicta was reared at lab condition, and incubated at 4 different temperature for 24h (10, 20, 30 and 40℃). 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: Totally 99,085 unigenes was obtained which at least 19,154 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 23 EggNOG terms resulted. DEGs with log2FC≥10 were screened and were compared at different temperatures. We found 203, 48 and 66 specific DEGs co-regulated at 10, 20 and 40℃, respectively compare with 30℃. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress. Conclusions: we compared the transcriptomes of S. invicta under high- and low-temperature stresses using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many high- and low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to RIFA overwintering and its behavior for adaptation in new environment as well as quarantine area.

Project description: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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Comparative transcriptome analysis of Solenopsis japonica (Hymenoptera: Formicidae) under low temperature and normal room temperature

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