CA Tabuloc, CR Carlson, F Ganjisaffar, H Zhang, CC Truong, C Chen, KM Lewald, S Hidalgo, FG Zalom, JC Chiu

Data generated from Illumina short-read sequencing (PE150) and PacBio long-read sequencing (Two 8M SMRT cells). RNA was extracted from isogenic lines developed from unsprayed Drosophila suzukii collected from populations resistant to either pyrethroid insecticide (specifically zeta-cypermethrin) or spinosad insecticide on either strawberries (S) or caneberries (C).

Female D. suzukii flies were entrained at 25C in 12-hour light:12-hour dark cycles for two full days. On the third day, flies were collected on dry ice sixteen hours after lights-on (ZT16). This time point was selected because D. suzukii was previously observed to exhibit a low level of cytochrome P450 expression at this time (Hamby et al., 2013). This means any overexpression may be more easily observed. Fly bodies were separated from heads using frozen metal sieves (Newark Wire Cloth Company, Clifton, New Jersey). Eight to ten female bodies were used per sample.

Zeta-cypermethrin-susceptible lines = S7, S8
Zeta-cypermethrin-resistant lines = S3, S4
Spinosad-susceptible lines = C2, C5
Spinosad-resistant lines = C3, C4

Differential gene expression (DEG analysis)
Differential gene expression analysis was performed using sequencing reads derived from Illumina short-read sequencing. First, rRNA reads were removed using SortMeRNA v2.1 (Kopylova et al., 2012). Adapters (ILLUMINACLIP parameters 2:30:10) and low-quality ends (LEADING: 10, TRAILING:10, MINLEN:36) were trimmed using Trimmomatic v0.35 (Bolger et al., 2014). Cleaned reads were aligned to the NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020) using STAR v2.7.9a (Dobin et al., 2013). Count data from STAR (--quantMode GeneCounts) served as input in the DESeq2 package (Love et al., 2014) in R to perform differential expression analysis on each resistant line vs all susceptible samples. Each resistant line was compared to susceptible samples separately as each line might exhibit resistance due to different mechanisms. Genes with fold change differences between resistant vs susceptible populations with a Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed. Expression levels of genes were also measured as fragments per kilobase of exon per million mapped (FPKM) values calculated with Stringtie v2.0.4 (Pertea et al., 2015). The consistency between biological replicates was calculated with Pearson’s correlation coefficient, which was determined with the ‘stats’ package in R version 4.2.1. Expression differences of key genes between the resistant and susceptible populations were calculated with two-way ANOVA followed by two-stage linear set-up procedure of Benjamini, Krieger, and Yekutieli on GraphPad Prism.

Weighted Gene Co-expression Network Analysis
Gene expression (in FPKM) served as input for Weighted Gene Co-expression Network Analysis (WGCNA). Genes with an expression value of zero for more than six samples were excluded from analysis. To explore the modules most correlated with insecticide resistance, a correlation analysis using resistance status was performed with the WGCNA package (Version 1.72.1) (Langfelder & Horvath, 2008) on R. Modules with a p-value < 0.05 were considered significant. Functional enrichment analysis (described below) was performed on the module with the highest correlation with resistance.

Functional enrichment analysis
Genes were functionally annotated using BLAST against the NCBI Drosophila melanogaster Annotation r6.32 based on the Release 6 plus ISO1 mitochondrial genome assembly (accession no. GCA_000001215.4) (dos Santos et al., 2015). Gene Ontology (GO) enrichment of genes were performed using ShinyGO 0.76.3 (Ge et al., 2020). GO terms and pathways were considered enriched if the false discovery rate (FDR) < 0.05.

Both 8M SMRT Cells of Iso-Seq data were pooled together and run through the isoseq3 pipeline (https://github.com/PacificBiosciences/IsoSeq, v. 3.8.0) to generate full-length non-chimeric (FLNC) isoform sequences. PolyA and concatemer sequences were removed from PacBio sequencing reads using ‘isoseq refine.’ To maximize detection of rare isoforms, both high-quality and low-quality FLNC isoform sequences were concatenated and mapped to the D. suzukii reference genome (accession no. GCF_013340165.1) (Paris et al., 2020) using minimap2 (H. Li, 2018) (v. 2.24-r1122; -ax splice -uf --secondary=no -C5). Mapped FLNC isoforms were then filtered and collapsed using cDNA_Cupcake (https://github.com/Magdoll/cDNA_Cupcake, collapse_isoforms_by_sam.py), retaining nonredundant isoforms. Nonredundant isoforms were classified against the reference genome and transcriptome using SQANTI3 QC v. 5.1 (Tardaguila et al., 2018). All short-read RNA-Seq data were used as evidence in SQANTI3 QC to validate isoforms. Isoforms flagged as artifacts by SQANTI3 QC were filtered using the SQANTI3 “rules” filter, retaining all full-splice matching isoforms not flagged as an intrapriming artifact and all non-full-splice matching isoforms not flagged as an intrapriming artifact, having a reverse-transcriptase-switching junction, and/or non-canonical splice junctions without short-read support. After filtering, SQANTI3 rescue was run to recover discarded reference transcripts that have long-read support, resulting in a final long-read supported transcriptome. This long-read transcriptome was then merged with the reference transcriptome to create a final, nonredundant expanded transcriptome. Splice junction and exon counts were then generated using Quality of RNA-Seq Tool-Set (QoRTs) (Hartley & Mullikin, 2015). Differential usage of exons and splice junctions was determined with JunctionSeq (Hartley & Mullikin, 2016). Features with FDR < 0.05 were considered differentially expressed/utilized.

Information for data tables

-Suppl. Table 2: Statistics for zeta-cypermethrin bioassay

Bioassays were performed to identify isogenic lines resistant to zeta-cypermethrin (Mustang® Maxx). Eight isogenic lines were tested (indicated as S#). Two isogenic lines from an untreated orchard (Wolfskill, W#) served as the susceptible control. Each biological replicate consisted of 5 males and 5 females (n=8). Significance was determined by one-way ANOVA followed by Tukey’s multiple comparison test.

-Suppl. Table 3: Statistics for spinosad bioassay

Bioassays were performed to identify isogenic lines resistant to spinosad (Entrust®). Eight isogenic lines were tested (indicated as C#). Two isogenic lines from an untreated orchard (Wolfskill, W#) served as the susceptible control. Each biological replicate consisted of 5 males and 5 females (n=8). Significance was determined by one-way ANOVA followed by Tukey’s multiple comparison test.

-Suppl. Table 5: DEGs in zeta-cypermethrin-resistant Drosophila suzukii (line S3)

List of differentially expressed genes (DEGs) in zeta-cypermethrin resistant line S3 as compared to susceptible lines S7 and S8. "SWD gene ID" and "SWD Gene Description" are based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "Dmel gene ID" is the Drosophila melanogaster gene symbol associated with each Dmel gene ID. "Log2FoldChange" is the difference in expression between the resistant line (S3) to both susceptible lines (S7 and S8--pooled together). Positive values indicate that the gene is upregulated in the resistant line while negative values indicate that the gene is downregulated in the resistant line. "padj" is the Benjamini-Hochberg adjusted p-value, and -log10(padj) is the log transformation of the adjusted p-values, where higher values indicate more significant fold change differences. Data is sorted into 3 tabs: genes that are upregulated, downregulated, and not significant. Genes with fold change differences between resistant vs susceptible populations with a Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed.

-Suppl. Table 6: DEGs in zeta-cypermethrin-resistant Drosophila suzukii (line S4)

List of differentially expressed genes (DEGs) in zeta-cypermethrin resistant line S4 as compared to susceptible lines S7 and S8. "SWD gene ID" and "SWD Gene Description" are based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "Dmel gene ID" is the Drosophila melanogaster gene symbol associated with each Dmel gene ID. "Log2FoldChange" is the difference in expression between the resistant line (S3) to both susceptible lines (S7 and S8--pooled together). Positive values indicate that the gene is upregulated in the resistant line while negative values indicate that the gene is downregulated in the resistant line. "padj" is the Benjamini-Hochberg adjusted p-value, and -log10(padj) is the log transformation of the adjusted p-values, where higher values indicate more significant fold change differences. Data is sorted into 3 tabs: genes that are upregulated, downregulated, and not significant. Genes with fold change differences between resistant vs susceptible populations with a Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed.

-Suppl. Table 7: Statistics comparing the expression of metabolic genes in zeta-cypermethrin-resistant vs. susceptible Drosophila suzukii

Relative expression (FPKM) of cytochrome P450 genes (Cyp), heat shock proteins (Hsp), the carboxylesterase Cricklet (Clt), and glutathione-s-transferase E3 (GstE3) in the susceptible (S7 and S8) vs resistant (S3 and S4) groups. There are a total of 3 biological replicates of 8-10 females per line. Significance was determined by 2-way ANOVA.

-Suppl. Table 8: Enrichment of DEGs in zeta-cypermethrin-resistant Drosophila suzukii (line S3)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes up- or down-regulated in line S3 (Suppl. Table 5). The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 9: Enrichment of DEGs in zeta-cypermethrin-resistant Drosophila suzukii (line S4)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes up- or down-regulated in line S4 (Suppl. Table 6). The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 10: Genes in all WGCNA modules for zeta-cypermethrin-resistant Drosophila suzukii (line S3)

To identify which genes in line S3 are most correlated with zeta-cypermethrin resistance, WGCNA was performed. Modules with a p-value < 0.05 were considered significant. The data table was produced by the WGCNA package (Version 1.72.1) (Langfelder & Horvath, 2008) on R. "Transcript" is the NCBI Reference Sequence ID, and "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSymbol" is the Drosophila melanogaster gene symbol associated with each Fbgn. "Module Color" is the clusters of highly interconnected genes. Modules correspond to clusters of genes with high absolute correlations. Gene significance (GS) is the correlation between gene expression and insecticide susceptibility. "p.GS.Susceptibility" is the p-value associate with the GS. Module membership (MM) is the association between gene expression and each module eigengene. The eigengene can be thought of as a weighted average expression profile. Finally, "p.MM" is the p-value associated with the Module Membership.

-Suppl. Table 11: Enrichment of the turquoise module in zeta-cypermethrin-resistant Drosophila suzukii (line S3)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes within the turquoise cluster. Turquoise was the cluster most correlated with zeta-cypermethrin resistance in line S3. The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 12: Genes in all WGCNA modules for zeta-cypermethrin-resistant Drosophila suzukii (line S4)

To identify which genes in line S4 are most correlated with zeta-cypermethrin resistance, WGCNA was performed. Modules with a p-value < 0.05 were considered significant. Data table was produced by the WGCNA package (Version 1.72.1) (Langfelder & Horvath, 2008) on R. "Transcript" is the NCBI Reference Sequence ID, and "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSymbol" is the Drosophila melanogaster gene symbol associated with each Fbgn. "Module Color" is the clusters of highly interconnected genes. Modules correspond to clusters of genes with high absolute correlations. Gene significance (GS) is the correlation between gene expression and insecticide susceptibility. "p.GS.Susceptibility" is the p-value associate with the GS. Module membership (MM) is the association between gene expression and each module eigengene. The eigengene can be thought of as a weighted average expression profile. Finally, "p.MM" is the p-value associated with the Module Membership.

-Suppl. Table 13: Enrichment of the turquoise module in zeta-cypermethrin-resistant Drosophila suzukii (line S4)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes within the turquoise cluster. Turquoise was the cluster most correlated with zeta-cypermethrin resistance in line S4. The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 14: DEGs in spinosad-resistant Drosophila suzukii (line C3)

List of differentially expressed genes (DEGs) in zeta-cypermethrin resistant line C3 as compared to susceptible lines C2 and C5. "SWD gene ID" and "SWD Gene Description" are based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "Dmel gene ID" is the Drosophila melanogaster gene symbol associated with each Dmel gene ID. "Log2FoldChange" is the difference in expression between the resistant line (C3) to both susceptible lines (C2 and C5--pooled together). Positive values indicate that the gene is upregulated in the resistant line while negative values indicate that the gene is downregulated in the resistant line. "padj" is the Benjamini-Hochberg adjusted p-value, and -log10(padj) is the log transformation of the adjusted p-values, where higher values indicate more significant fold change differences. Data is sorted into 3 tabs: genes that are upregulated, downregulated, and not significant. Genes with fold change differences between resistant vs susceptible populations with a Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed.

-Suppl. Table 15: DEGs in spinosad-resistant Drosophila suzukii (line C4)

List of differentially expressed genes (DEGs) in zeta-cypermethrin resistant line C4 as compared to susceptible lines C2 and C5. "SWD gene ID" and "SWD Gene Description" are based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "Dmel gene ID" is the Drosophila melanogaster gene symbol associated with each Dmel gene ID. "Log2FoldChange" is the difference in expression between the resistant line (C4) to both susceptible lines (C2 and C5--pooled together). Positive values indicate that the gene is upregulated in the resistant line while negative values indicate that the gene is downregulated in the resistant line. "padj" is the Benjamini-Hochberg adjusted p-value, and -log10(padj) is the log transformation of the adjusted p-values, where higher values indicate more significant fold change differences. Data is sorted into 3 tabs: genes that are upregulated, downregulated, and not significant. Genes with fold change differences between resistant vs susceptible populations with a Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed.

-Suppl. Table 16: Statistics comparing the expression of metabolic and cuticular genes in spinosad-resistant vs. susceptible Drosophila suzukii

Relative expression (FPKM) of metabolic and cuticular genes (twdl: tweedle; cpr: cuticular protein) in the susceptible (C2 and C5) and resistant (C3 and C4) groups.There are a total of 3 biological replicates of 8-10 females per line. Significance was determined by 2-way ANOVA.

-Suppl. Table 17: Enrichment of DEGs in spinosasd-resistant Drosophila suzukii (line C3)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes up- or down-regulated in line C3 (Suppl. Table 14). The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 18: Enrichment of DEGs in spinosad-resistant Drosophila suzukii (line C4)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes up- or down-regulated in line C4 (Suppl. Table 15). The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 19: Genes in all WGCNA modules for spinosasd-resistant Drosophila suzukii (line C3)

To identify which genes in line C3 are most correlated with spinosad resistance, WGCNA was performed. Modules with a p-value < 0.05 were considered significant. Data table was produced by the WGCNA package (Version 1.72.1) (Langfelder & Horvath, 2008) on R. "Transcript" is the NCBI Reference Sequence ID, and "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSymbol" is the Drosophila melanogaster gene symbol associated with each Fbgn. "Module Color" is the clusters of highly interconnected genes. Modules correspond to clusters of genes with high absolute correlations. Gene significance (GS) is the correlation between gene expression and insecticide susceptibility. "p.GS.Susceptibility" is the p-value associate with the GS. Module membership (MM) is the association between gene expression and each module eigengene. The eigengene can be thought of as a weighted average expression profile. Finally, "p.MM" is the p-value associated with the Module Membership.

-Suppl. Table 20: Genes in all WGCNA modules for spinosasd-resistant Drosophila suzukii (line C4)

To identify which genes in line C4 are most correlated with spinosad resistance, WGCNA was performed. Modules with a p-value < 0.05 were considered significant. Data table was produced by the WGCNA package (Version 1.72.1) (Langfelder & Horvath, 2008) on R. "Transcript" is the NCBI Reference Sequence ID, and "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSymbol" is the Drosophila melanogaster gene symbol associated with each Fbgn. "Module Color" is the clusters of highly interconnected genes. Modules correspond to clusters of genes with high absolute correlations. Gene significance (GS) is the correlation between gene expression and insecticide susceptibility. "p.GS.Susceptibility" is the p-value associate with the GS. Module membership (MM) is the association between gene expression and each module eigengene. The eigengene can be thought of as a weighted average expression profile. Finally, "p.MM" is the p-value associated with the Module Membership.

-Suppl. Table 21: Enrichment of the green module in spinosasd-resistant Drosophila suzukii (line C4)

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for genes within the green cluster. Green was the cluster most correlated with spinosad resistance in line C4. The table was produced by ShinyGo (Ge et al., 2020). "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

-Suppl. Table 22: Differential usage of splice junctions, exons, and introns in insecticide-resistant Drosophila suzukii

Differential usage of splice junctions, exons, and introns for each resistant D. suzukii line to both susceptible lines was determined using JunctionSeq (Hartley & Mullikin, 2016). Alternative splicing (AS) events for each line is in a separate tab. AS categories include Exon Skipping (ES), Exon Inclusion (EI), Intron Retention (IR), and Alternative splice site (Altss). "Gene ID" is the D. suzukii gene ID from the updated transcriptome reference. "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Novel" indicates that the gene was not previously annotated in the LBDM_Dsuz_2.1.pri assembly. "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSym" is the Drosophila melanogaster gene symbol associated with each Fbgn. The remainder of the table is an output from JunctionSeq. A full description of each column can be found on pages 14-15 of the JunctionSeq User Manual: http://hartleys.github.io/JunctionSeq/doc/JunctionSeq.pdf.

-Suppl. Table 23: Pairwise comparisons of differentially spliced genes

Differential usage of splice junctions, exons, and introns for pairwise comparisons between each resistant D. suzukii line to each susceptible line was determined using JunctionSeq (Hartley & Mullikin, 2016). Alternative splicing (AS) events for each line is in a separate tab. AS categories include Exon Skipping (ES), Exon Inclusion (EI), Intron Retention (IR), Alternative splice site (Altss). "Gene ID" is the D. suzukii gene ID from the updated genome annotation. "LOC" is the SWD gene ID based off of NCBI Drosophila suzukii Annotation Release 102 based on the LBDM_Dsuz_2.1.pri assembly (accession no. GCF_013340165.1) (Paris et al., 2020). "Novel" indicates that the gene was not previously annotated in the LBDM_Dsuz_2.1.pri assembly. "Fbgn" is the FlyBase Gene ID that is most similar (by sequence similarity) to the SWD gene ID. "GeneSym" is the Drosophila melanogaster gene symbol associated with each Fbgn. The remainder of the table is an output from JunctionSeq. A full description of each column can be found on pages 14-15 of the JunctionSeq User Manual: http://hartleys.github.io/JunctionSeq/doc/JunctionSeq.pdf.

-Suppl. Table 24: Enrichment of differentially spliced genes

Enrichment pathways within the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) Biological Processes (bio proc) categories for differentially spliced genes from each pairwise comparison (Suppl. Table 23). The table was produced using ShinyGo. "Enrichment FDR" (where FDR is the false discovery rate) is adjusted from the hypergeometric test. "nGenes" is number of differentially expressed genes that belong to the indicated pathway while "Pathway Genes" indicate the total number of genes that make up that pathway. "Fold Enrichment" is defined as the percentage of genes in your list belonging to a pathway, divided by the corresponding percentage in the background. FDR tells us how likely the enrichment is by chance. "Fold Enrichment" indicates how drastically genes of a certain pathway is overrepresented. "Pathway" is the name of the enriched pathway, and "URL" provides information on that pathway. Finally, "Genes" provides a list of differentially expressed genes that are in each pathway.

Note: Missing values are denoted by NA.

Raw Data can be found under BioProject PRJNA983428