Comparative transcriptome analysis of Solenopsis japonica (Hymenoptera: Formicidae) under low temperature and normal room temperature
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ABSTRACT:
PROVIDER: PRJNA649847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12358186_1.fastq.gz | Fastqsanger.gz | |||
| SRR12358186_2.fastq.gz | Fastqsanger.gz | |||
| SRR12358187_1.fastq.gz | Fastqsanger.gz | |||
| SRR12358187_2.fastq.gz | Fastqsanger.gz |
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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 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.
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Project description:A Solenopsis clade including Solenopsis invicta, Solenopsis richteri, Solenopsis macdonaghi, Solenopsis sp, Solenopsis megergates, Solenopsis geminata, Solenopsis saevissima, Solenopsis pusilligni, Solenopsis daguerrei, Solenopsis nr. nigella Genome
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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.
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Project description:Neonicotinoid insecticides are commonly used in managing pest insects, including the imported fire ant, Solenopsis invicta Buren. There is increasing evidence that neonicotinoid insecticides at sublethal concentrations have profound effects on social insects. However, the sublethal effect of neonicotinoids on S. invicta has never been investigated. In this study, the newly mated queens were fed with water containing 0.01 or 0.25 ?g/ml imidacloprid. Imidacloprid at both concentrations did not cause any increase in queen mortality during the founding stage; however, it significantly reduced queens' brood tending ability. In the 0.25 ?g/ml imidacloprid treatment, the time to larval emergence was significantly delayed and no pupae or adult workers were produced. This study provides clear evidence that imidacloprid at sublethal concentrations has a significant detrimental impact on S. invicta queens and the development of incipient colonies.
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Project description:Ants provide remarkable examples of equivalent genotypes developing into divergent and discrete phenotypes. Diploid eggs can develop either into queens, which specialize in reproduction, or workers, which participate in cooperative tasks such as building the nest, collecting food, and rearing the young. In contrast, the differentiation between males and females generally depends upon whether eggs are fertilized, with fertilized (diploid) eggs giving rise to females and unfertilized (haploid) eggs giving rise to males. To obtain a comprehensive picture of the relative contributions of gender (sex), caste, developmental stage, and species divergence to gene expression evolution, we investigated gene expression patterns in pupal and adult queens, workers, and males of two species of fire ants, Solenopsis invicta and Solenopsis richteri. Microarray hybridizations revealed that variation in gene expression profiles is influenced more by developmental stage than by caste membership, sex, or species identity. The second major contributor to variation in gene expression was the combination of sex and caste. Although workers and queens share equivalent diploid nuclear genomes, they have highly distinctive patterns of gene expression in both the pupal and the adult stages, as might be expected given their extraordinary level of phenotypic differentiation. Overall, the difference in the proportion of differentially expressed genes was greater between workers and males than between workers and queens or queens and males, consistent with the fact that workers and males share neither gender nor reproductive capability. Moreover, between-species comparisons revealed that the greatest difference in gene expression patterns occurred in adult workers, a finding consistent with the fact that adult workers most directly experience the distinct external environments characterizing the different habitats occupied by the two species. Thus, much of the evolution of gene expression in ants may occur in the worker caste, despite the fact that these individuals are largely or completely sterile. Analyses of gene expression evolution revealed a combination of positive selection and relaxation of stabilizing selection as important factors driving the evolution of such genes. Transcriptome analysis is a powerful tool for unveiling the distribution and magnitude of genetic incompatibilities between hybridizing taxa. The nature of such incompatibilities is closely associated with the evolutionary histories of the parental species and may differ across tissues and between the sexes. In eusocial insects, the presence of distinct castes that experience divergent selection regimes may result in additional distinct patterns of caste-specific hybrid incompatibilities. We analyzed levels of expression of >14,000 genes in two life stages of each caste and sex in the fire ants Solenopsis invicta and Solenopsis richteri and in their hybrids. We found strong contributions of both developmental stage and caste to gene expression patterns. In contrast, variability in expression was only weakly associated with species, with hybrid scores falling between those of the two parental species in both life stages and all castes. Hybrid incompatibilities were surprisingly modest, with only 16 genes in pupae and 18 genes in adults being mis-expressed, and indicating low levels of disruption in gene regulation in hybrids. The castes differed in numbers of mis-expressed genes, with males and workers each mis-expressing at least seven times as many genes as queens in both life stages. Interestingly, homologues of many of the mis-expressed genes have been implicated in behavioral variation in Drosophila melanogaster. General expression profiles of hybrids consistently were more similar to those of Solenopsis richteri than Solenopsis invicta, presumably because Solenopsis richteri trans-regulatory elements tend to be dominant to those of Solenopsis invicta and/or because there is an overall bias in the genetic composition of the hybrids towards Solenopsis richteri. Altogether, our results suggest that selection acting on each caste may contribute differently to interspecific divergence and speciation in this group of ants.
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