Dataset DOI: 10.5061/dryad.r4xgxd2vx

Description of the data and file structure

This dataset contains the supporting data underlying the manuscript entitled "Geomagnetic intensity variation and deprivation elicit distinct transcriptomic responses in a migratory insect".

We deposited the raw and processed data supporting the transcriptomic analyses, functional enrichment analyses, RT-qPCR validation, RNA interference experiments, and magnetic field measurements presented in the manuscript.

Brown planthoppers, Nilaparvata lugens (Stal), were exposed to different magnetic field conditions, including geomagnetic field intensities of approximately 45 uT and 50 uT, representing natural-range geomagnetic intensity variation experienced during migration, and a near-zero magnetic field (NZMF) condition. RNA sequencing was performed to investigate transcriptomic responses under different magnetic field environments.

The dataset includes gene expression count matrices, differential expression analysis results, functional enrichment analysis results, magnetic field parameter measurements, RT-qPCR validation data, and RNA interference-based functional validation data.

The following files are included in this dataset:

Raw_data_for_RNAseq_count_matrix.csv contains the gene-level read count matrix generated from RNA sequencing and used for transcriptomic analysis.

Raw_data_for_Figure1-Complete list of differentially expressed genes in all comparisons.xlsx contains the complete DESeq2 differential expression analysis results for the three pairwise comparisons among the magnetic field treatments.

Raw_data_for_Figure2-Functional enrichment of transcriptional responses under different magnetic field conditions.xlsx contains the functional enrichment analysis results, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

Raw_data_for_Figure3-RT-qPCR validation of representative genes responding to different magnetic field conditions.xlsx contains RT-qPCR validation data for representative differentially expressed genes identified from transcriptomic analyses.

Raw_data_for_Figure4-Cry1 knockdown disrupts diel eclosion rhythmicity in female brown planthopper.xlsx contains RNA interference experimental data used to evaluate the functional role of Cry1 in regulating eclosion rhythm.

Raw_data_for_FigureS1-Control of magnetic field parameters under different magnetic field treatments.xlsx contains measured magnetic field parameters, including magnetic field intensity, declination, and inclination.

The deposited data support all statistical analyses, results, tables, and figures presented in the associated manuscript.

Files and variables

File: Dataset_supporting_manuscript.zip

Raw_data_for_RNAseq_count_matrix.csv

Data brief description: This file contains the gene-level read count matrix generated from RNA sequencing of brown planthoppers exposed to different magnetic field conditions. The count matrix was used as the input for downstream transcriptomic analyses, including differential expression analysis. The values represent the number of sequencing reads assigned to each gene and are dimensionless.

The variables are described as follows:

Gene_Symbol: Gene identifier.

Sample columns: RNA-seq samples under different magnetic field treatments. The values represent the number of sequencing reads assigned to each gene.

The naming of different samples is as follows:

GMF45: Geomagnetic field treatment with a magnetic field intensity of approximately 45 μT.

GMF50: Geomagnetic field treatment with a magnetic field intensity of approximately 50 μT.

NZMF: Near-zero magnetic field treatment.

The suffixes _1, _2, and _3 represent independent biological replicates.

NZMF_3 is included in the gene count matrix but was excluded from downstream transcriptomic analyses because this library did not meet the quality-control criteria. Therefore, downstream analyses were performed using three GMF45 replicates, three GMF50 replicates, and two NZMF replicates.

Raw_data_for_Figure1-Complete list of differentially expressed genes in all comparisons.xlsx

Data brief description: In Figure 1, we compared transcriptomic responses of brown planthoppers under different magnetic field conditions. This file contains the complete DESeq2 differential expression analysis results for GMF50 versus GMF45, NZMF versus GMF45, and NZMF versus GMF50. Each sheet represents one pairwise comparison. The complete DESeq2 output is provided without pre-filtering according to the differential expression threshold.

The variables are described as follows:

GeneSymbol: Gene identifier.

baseMean: Mean normalized count across the samples included in the DESeq2 analysis.

log2FoldChange: Estimated log2 fold change in gene expression between the two comparison groups.

lfcSE: Standard error of the estimated log2 fold change.

stat: Wald test statistic calculated by DESeq2.

pvalue: P-value from the Wald test before multiple-testing correction.

padj: P-value adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) method.

NA values in the pvalue or padj columns indicate genes for which statistical significance was not available in DESeq2, for example because of insufficient expression information or independent filtering.

The naming of different comparisons is as follows:

DEG_GMF50_vs_GMF45: Gene expression under GMF50 μT relative to GMF45 μT.

DEG_NZMF_vs_GMF45: Gene expression under NZMF relative to GMF45 μT.

DEG_NZMF_vs_GMF50: Gene expression under NZMF relative to GMF50 μT.

Raw_data_for_Figure2-Functional enrichment of transcriptional responses under different magnetic field conditions.xlsx

Data brief description: In Figure 2, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to characterize functional changes associated with transcriptional responses under different magnetic field conditions. This file contains the source data used for the functional enrichment analyses shown in Figure 2. Each sheet corresponds to the respective panel and contains either GO or KEGG enrichment results for the corresponding magnetic field comparison.

For GO enrichment analysis, the variables are described as follows:

ONTOLOGY: GO ontology category, including Biological Process (BP), Molecular Function (MF), and Cellular Component (CC).

ID: GO term accession identifier.

Description: Functional description of the GO term.

GeneRatio: Ratio of input genes associated with the GO term.

BgRatio: Ratio of background genes associated with the GO term.

RichFactor: Enrichment ratio based on the proportions of input and background genes associated with the GO term.

FoldEnrichment: Fold enrichment of the GO term relative to the background gene set.

zScore: Standardized enrichment score.

pvalue: P-value of the enrichment test before multiple-testing correction.

p.adjust: Benjamini-Hochberg adjusted P-value.

qvalue: Estimated false discovery rate (FDR) q-value.

geneID: Gene identifiers contributing to the enriched GO term.

Counts: Number of input genes associated with the GO term.

For KEGG pathway enrichment analysis, the variables are described as follows:

category: KEGG pathway category.

subcategory: KEGG pathway subcategory.

ID: KEGG pathway identifier.

Description: Description of the enriched KEGG pathway.

GeneRatio: Ratio of input genes associated with the KEGG pathway.

BgRatio: Ratio of background genes associated with the KEGG pathway.

RichFactor: Enrichment ratio based on the proportions of input and background genes associated with the KEGG pathway.

FoldEnrichment: Fold enrichment of the KEGG pathway relative to the background gene set.

zScore: Standardized enrichment score.

pvalue: P-value of the enrichment test before multiple-testing correction.

p.adjust: Benjamini-Hochberg adjusted P-value.

qvalue: Estimated false discovery rate (FDR) q-value.

geneID: Gene identifiers contributing to the enriched KEGG pathway.

Count: Number of input genes associated with the KEGG pathway.

The naming of treatment comparisons follows the same definitions as described for Figure 1.

Raw_data_for_Figure3-RT-qPCR validation of representative genes responding to different magnetic field conditions.xlsx

Data brief description: In Figure 3, we used RT-qPCR to validate the expression patterns of representative genes identified from the transcriptomic analyses under different magnetic field conditions. Each treatment contained three independent biological replicates. Relative gene expression was calculated using the 2^-ΔΔCt method.

The variables are described as follows:

Gene Symbol: Gene identifier of the target gene analyzed by RT-qPCR.

GMF45_1–GMF45_3, GMF50_1–GMF50_3, and NZMF_1–NZMF_3: Relative expression levels of candidate genes calculated using the 2^-ΔΔCt method for three independent biological replicates under the corresponding magnetic field treatments.

log2FC: Log2 fold change between the two treatment groups, calculated as the difference between the mean log2-transformed relative expression values of the two groups:

log2FC = mean[log2(Group 1)] - mean[log2(Group 2)]

SE_log2FC: Standard error of the estimated log2 fold change, calculated as:

SE_log2FC = sqrt(SD1²/n1 + SD2²/n2)

where SD1 and SD2 are the standard deviations of the log2-transformed relative expression values in the two treatment groups, and n1 and n2 are the numbers of biological replicates. In this study, n1 = n2 = 3.

The naming of different samples is as follows:

GMF45, GMF50, and NZMF: The corresponding magnetic field treatments.

The suffixes _1, _2, and _3 represent three independent biological replicates.

For example, GMF50_1 represents the first biological replicate under the GMF50 treatment.

Raw_data_for_Figure4-Cry1 knockdown disrupts diel eclosion rhythmicity in female brown planthopper.xlsx

Data brief description: In Figure 4, we used RNA interference to evaluate the functional role of Cry1 in diel eclosion rhythmicity in female brown planthoppers. Cry1 expression after dsRNA treatment was measured by RT-qPCR, and eclosion events were subsequently recorded under the corresponding treatments.

The variables are described as follows:

For Figure 4A and Figure 4B:

Treatment: dsRNA treatment group.

2^-ΔΔCt: Relative expression level of Cry1 calculated using the 2^-ΔΔCt method.

Figure 4A shows Cry1 expression in second-day fifth-instar nymphs, whereas Figure 4B shows Cry1 expression in 2-day-old female adults.

For Figure 4C and Figure 4D:

ZT: Zeitgeber time. ZT0 corresponds to light onset at 08:00, and ZT14 corresponds to dark onset at 22:00.

Eclosion number: Number of females that eclosed during the corresponding 2-h observation interval.

Eclosion ratio (%): Percentage of females that eclosed during the corresponding 2-h observation interval.

Eclosion events were recorded at 2-h intervals under the dsGFP and dsCry1 treatments.

The naming of different treatments is as follows:

dsGFP: Control group injected with dsRNA targeting GFP.

dsCry1: Treatment group injected with dsRNA targeting Cry1.

Raw_data_for_FigureS1-Control of magnetic field parameters under different magnetic field treatments.xlsx

Data brief description: In Figure S1, we characterized the magnetic field parameters under different experimental magnetic field treatments. Magnetic field intensity was measured under the GMF50, GMF45, and NZMF treatments, whereas magnetic declination and inclination were measured under the GMF50 and GMF45 treatments.

The variables are described as follows:

For Figure S1A:

Magnetic field intensity (μT) : Total magnetic field intensity measured under the GMF50, GMF45, and NZMF treatments.

For Figure S1B:

MagneticDeclination (°): Magnetic declination measured under the GMF50 and GMF45 treatments. The values in the deposited dataset retain their directional signs. For graphical presentation in Figure S1B of the manuscript, the absolute values of magnetic declination were used.

For Figure S1C:

MagneticInclination (°): Magnetic inclination measured under the GMF50 and GMF45 treatments.

The naming of different treatments is as follows:

GMF45: Geomagnetic field treatment with a magnetic field intensity of approximately 45 μT.

GMF50: Geomagnetic field treatment with a magnetic field intensity of approximately 50 μT.

NZMF: Near-zero magnetic field treatment.

Magnetic declination and inclination were not characterized under the NZMF treatment because the total magnetic field intensity was reduced to near zero, making the magnetic field direction insufficiently stable or meaningful for defining directional parameters.

Code/software

File: Code_for_this_manuscript.zip

GO and KEGG enrichment analyses were performed using the clusterProfiler package in R. No additional P-value or q-value cutoff was applied to the enrichment results. For visualization, enriched terms were ranked according to their nominal enrichment P-values. GO enrichment plots were generated in R, whereas KEGG enrichment results were visualized using GraphPad Prism.

Code_for_DESeq2_PCA_and_volcano_plots.R

Script description: This R script processes the RNA-seq count matrix and performs differential expression analysis among the GMF45, GMF50, and NZMF treatment groups. The sample NZMF_3 was excluded from downstream analyses due to quality-control considerations. Genes with a total read count of at least 6 across all retained samples were retained for analysis. Differential expression analysis was performed using DESeq2 for the comparisons GMF50 vs GMF45, NZMF vs GMF45, and NZMF vs GMF50. Differentially expressed genes were identified using the thresholds |log2FoldChange| > 0.25 and adjusted P < 0.05. The script also performs principal component analysis (PCA), summarizes the numbers of differentially expressed genes, and generates volcano plots.

The input data source is described as follows:
Raw_data_for_RNAseq_count_matrix.csv: Raw gene-level RNA-seq count matrix used for differential expression analysis and PCA.

The outputs are described as follows:
Raw_data_for_Figure1-Complete list of differentially expressed genes in all comparisons.xlsx: Complete DESeq2 results for the comparisons GMF50 vs GMF45, NZMF vs GMF45, and NZMF vs GMF50.

The script also calculates the numbers of up-regulated, down-regulated, and total differentially expressed genes, as well as PCA and volcano plots. These results are derived directly from the RNA-seq count matrix and the complete DESeq2 results using the thresholds specified above.

Code_for_GO_KEGG_enrichment_analysis.R

Script description: This R script performs Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for differentially expressed genes from the three pairwise comparisons: GMF50 vs GMF45, NZMF vs GMF45, and NZMF vs GMF50. Gene symbols are converted to Entrez gene IDs using the Nilaparvata lugens annotation resource (AnnotationHub accession AH118659). GO enrichment analysis is performed for the biological process (BP), cellular component (CC), and molecular function (MF) categories, and KEGG pathway enrichment analysis is performed using clusterProfiler. The script exports the complete GO and KEGG enrichment results for the three comparisons and generates GO enrichment plots.

The input data source is described as follows:
Raw_data_for_Figure1-Complete list of differentially expressed genes in all comparisons.xlsx: Complete DESeq2 results for the three pairwise comparisons. Differentially expressed genes used for GO and KEGG enrichment analyses were selected from this file using the thresholds |log2FoldChange| > 0.25 and adjusted P < 0.05.

The output file is described as follows:
Raw_data_for_Figure2-Functional enrichment of transcriptional responses under different magnetic field conditions.xlsx: Complete GO and KEGG enrichment results for the three pairwise comparisons.

The script also generates GO enrichment plots for the three pairwise comparisons. 

Access information

Other publicly accessible locations of the data:

• NCBI Sequence Read Archive (SRA), BioProject PRJNA1469985: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1469985/

Data was derived from the following sources:

• Not applicable