This document is intended to supplement the Materials and Methods provided in the main article text. Scripts and related files can be found at https://github.com/aphanotus/morphDE.

Sampling design

Soapberry bugs were collected from multiple field locations in the United States and reared in the lab as described by Fawcett et al. (2018). Transcriptome studies proceeded through three phases. Initially, we sampled whole bodies from 12 individuals, including three biological replicates of each sex-and-morph combination from the Plantation Key, FL population (phase 1). Next we sampled dorsal thorax and gonads from three individuals of each sex-and-morph combination from the Plantation Key, FL and Aurora, CO populations (phase 2). The head, thorax and abdomen were separated in transverse sections with a scalpel. The thorax was then bisected in a frontal section, just dorsal of the base of the legs. The ventral thorax was discarded. The gonads were then removed from the adult abdomen using forceps. Because juvenile gonads are very small, we instead sampled the juvenile abdomen after removing the gut. Samples from these phases were prepared as full-length 150-bp, paired-end Illumina libraries and used to assemble a reference transcriptome. The final project phase utilized 3’-tag sequencing with the exclusive goal of quantifying gene expression. The sampling design at this phase included two stages (fifth instars and nascent adults), two tissues (dorsal thorax and gonads), two sexes, long- and short-wing adult morphs, high and low food regimes, four populations (collected from Key Largo, FL, Plantation Key, FL, Aurora, CO, and Frederick, MD), and three biological replicates of each unique combination of the preceding factors. The influence of population was not examined in this study. Instead sampling across populations ensures that any results apply broadly for the species. The full matrix contained 288 samples. Juveniles cannot be distinguished as presumptive long- or short-winged adults, even by morphometric analysis of the fifth instar wing pads. (Therefore the full design is 2 × 2 × 2 × 1.5 × 2 × 4 × 3 = 288.) Seven samples were lost or did not pass library quality controls, resulting in 281 samples in the analysis. Individual bugs were raised under a range of food density conditions (Fig. S1). Modeling was performed using both continuous food density values and by categorizing bugs raised with more or less than one seed per bug into high or low food regimes, respectively.

Fig. S1

The distribution of food density experienced by individuals in this study was intended to be continuous and bimodal. Bugs raised with one or more seeds per bug were categorized as part of the high food regime (light gray background). Those with less than one seed per bug were consideration part of the low food regime (dark gray background). Juvenile survival in isolation is very low. Therefore bugs are raised in cohorts. Cohort size deciles in this study are indicated by color in the bars.

Shape analysis

Wing landmarks were taken from Fawcett et al. (2018) and are described in Table S1.

Table S1 Wing landmark positions

landmark position
1 Bifurcation of the radial and medial veins
2* Maximum curvature of clavus, near the posterior tip of the mesonotum
3-4* Two equally spaced semilandmarks along the claval margin, anterior of landmark 2
5 Bifurcation of the radial vein and R2 crossvein
6 Intersection of the R2 crossvein and the medial vein
7 Intersection of the cubitus vein and the first anal vein
8* One semilandmark along the claval margin, between landmarks 2 and 7
9 Intersection of the medial vein and the posterior crossvein
10 Intersection of the radial vein and the anterior crossvein
11 Terminus of the radial-medial crossvein
12 First branch of the anterior membrane vein
13* Maximum posterior-distal curvature of the membrane region of the wing (roughly lateral to landmark 11 when held in place on the bug)
14-16* Three equally spaced semilandmarks along the posterior wing margin, between landmarks 7 and 13
17-21* Five equally spaced semilandmarks along the distal wing margin, between landmarks 11 and 13
22-24* Three equally spaced semilandmarks along the anterior wing margin, between landmarks 1 and 11
* semilandmark

This system of landmarks was adapted to quantify juvenile wing pad shapes as described in Table S2.

Table S2 Juvenile wing pad landmark positions.

landmark position
1 Bifurcation of the radial and medial veins
2 Medial base of the wing pad
3-4* Two equally spaced semilandmarks along the base of the wing pad, at its attachment to the body, between landmarks 1 and 2
5 Bifurcation of the radial vein and R2 crossvein
6 Intersection of the R2 crossvein and the medial vein
7 Intersection of the cubitus vein and the first anal vein
8* One semilandmark along the claval margin, between landmarks 2 and 7
9 Intersection of the medial vein and the posterior crossvein
10 Intersection of the radial vein and the anterior crossvein
11 Terminus of the radial-medial crossvein
12* Maximum posterior-distal curvature of the wing (roughly lateral to landmark 11)
13* One equally spaced semilandmark along the posterior wing margin, between landmarks 7 and 12
14-18* Five equally spaced semilandmarks along the distal wing margin, between landmarks 12 and 11
19-21* Three equally spaced semilandmarks along the anterior wing margin, between landmarks 1 and 11
* semilandmark

Thorax shapes of juvenile and adult bugs were digitized using the same set of landmarks (Table S3) .

Table S3 Thorax landmark positions.

landmark position
1 Anterior right of the pronotum, as viewed from above
2 Posterior right of the pronotum
3 Posterior left of the pronotum
4 Anterior left of the pronotum
5 Anterior midline of the pronotum
6 Anterior left of the mesonotum
7 Anterior midline of the mesonotum
8 Anterior right of the mesonotum
9 Posterior of the mesonotum

Variation in shapes was analyzed using the geometric morphometric methods implemented in the R packages geomorph and borealis. Generalized Procrustes analysis with partial Procrustes superimposition was preformed using minimized bending energy. The shape of individual specimens was quantified along the first principle component axis (Fig. S2B, S3B). Procrustes ANOVA with permutation was used to assess hypotheses for patterns of shape variation among the aligned specimens, using 10,000 iterations.

Fig. S2

Morphospace plotting the first two principle component axes for the shapes of juvenile wing pads (A) and adult wings (B). Specimens are color-coded by sex and morph (for adults), and colored convex hulls show the space occupied by these groups. Deformation grids illustrate shapes at the extremes of each axis. (Anterior is up; distal is right.) The percent of total shape variance described by each principle component in given on the axis. Abbreviations: LW, long-winged; SW, short-winged; f, female; m, male.

Fig. S3

Morphospace plotting the first two principle component axes for the shapes of juvenile (A) and adult (B) pronotum and mesonotum. Specimens are color-coded by sex and morph (for adults), and colored convex hulls show the space occupied by these groups. Deformation grids illustrate shapes at the extremes of each axis. (Anterior is up.) The percent of total shape variance described by each principle component in given on the axis. Abbreviations: LW, long-winged; SW, short-winged; f, female; m, male.

Sequencing and assembly of a reference transcriptome

Samples used for transcriptome assembly (phases 1 and 2) were delivered on dry ice to Beckman Coulter Genomics (Danvers, Massachusetts) for poly-A selection, preparation of 125 bp paired-end TruSeq libraries, and sequencing using Illumina HiSeq. Libraries from phases 1 and 2 were sequenced separately. Reads from all samples were trimmed using Trimmomatic version 0.33 (Bolger et al. 2014) with the parameters ILLUMINACLIP:/export/local/src/Trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:30:10 HEADCROP:12 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:15 MINLEN:50. The resulting reads were assembled into transcripts by Trinity version 2.0.6 (Grabherr et al. 2011). Before annotation, potentially redundant transcripts with greater than 90% identity were collapsed using CD-HIT-EST version 4.6 (Li & Godzik 2006).

cd /research/drangeli/phase2_BCG_RNAseq/Jhae_GU_trinity_assembly/
cd-hit-est -i GU.Trinity.fa -o GU.Trinity.c90.fa -c 0.90 -n 10 -d 0 -M 64000 -T 12

TransDecoder identified coding sequences. At each stage, BUSCO version 5.2.2 (Manni et al. 2021) was used to assess transcriptome completeness.

busco --in GU.Trinity.fa \
--lineage_dataset /research/drangeli/DB/busco.lineages/hemiptera_odb10 \
--out BUSCO.report.for.GU \
--augustus --augustus_species fly --mode transcriptome --cpu 24

Consolidation by cd-hist-est dramatically reduced the number of sequences flagged as duplicates (Table S4).

Table S4 Assembly details at each stage of processing.

dataset contigs BUSCO short summary
initial assembly 549,485 C:97.0%[S:54.2%,D:42.8%],F:1.3%,M:1.7%,n:2510
initial assembly CDS 85,937
90% consolidation 395,125 C:96.6%[S:77.7%,D:18.9%],F:1.4%,M:2.0%,n:2510
90% consolidation CDS 50,771 C:94.4%[S:77.8%,D:16.6%],F:2.2%,M:3.4%,n:2510

Annotation of the transcriptome

Transcript annotation was performed by EnTAP (Hart et al. 2019) using the NCBI invertebrate RefSeq dataset, SwissProt and Trembl databases. EnTAP assigns sequence names and GO terms based on similarity.

EnTAP --runP --threads 24 \
-i /research/drangeli/phase2_BCG_RNAseq/Jhae_GU_trinity_assembly/GU.Trinity.c90.fa \
-d /export/groups/drangeli/entap_config/bin/invert.dmnd \
-d /export/groups/drangeli/entap_config/bin/uniprot_sprot.dmnd \
-d /export/groups/drangeli/entap_config/bin/uniprot_trembl.dmnd \
--ini /export/groups/drangeli/Jhae.genome/entap_config.ini

The J. haematoloma sequences were matched to other Hemiptera, primarily Halyomorpha halys, Cimex lectularius and Nilaparvata lugens for the RefSeq comparisons and Oncopeltus, Lygus and Riptortus from TrEMBL. The contaminant sequence species are also as expected, coming from bacteria and yeasts.

Sequencing for gene expression quantification

For gene expression analysis, RNA samples were shipped overnight on dry ice to the DNA Technologies Core at the University of California at Davis. Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Greenland, New Hampshire, USA) in the three batches for sequencing in separate Illumina HiSeq lanes. Batch 3 was sequenced twice and reads counts for each run were added together for each sample after filtering.

These batches were sequenced in three lanes yielding 115.9×109 bp. All raw short read data and sample metadata used in this study are available under NCBI BioProject PRJNA845792. Short read sequences were inspected for quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), before and after trimmed using Trimmomatic version 0.33, as in the example command below.

java -jar trimmomatic-0.33.jar SE \
raw.data/A1-d25-2_S161_L006_R1_001.fastq \
filtered.reads/A1-d25-2_S161_L006_R1_001.trimmed.fastq \
ILLUMINACLIP:/export/local/src/Trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:30:10 \
HEADCROP:16 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:15 MINLEN:79

A simple bash script was used to apply trimming to all read files and save the output in a separate folder. FastQC inspection after trimming revealed notable improvements.

Table S5 Read numbers before and after quality filtering.

batch raw reads filtered reads passing filter
1 341,370,316 323,188,378 94.7%
2 321,564,969 313,590,249 97.5%
3 484,588,962 419,931,564 86.7%
overall 1,147,524,247 1,056,710,191 92.1%

Mapping 3seq reads to the transcriptome

Kallisto was used to quantify the abundance of transcripts from 3seq data using a pseudo-alignment method (Bray et al. 2016). First, a Kallisto index was created from the assembled transcripts, collapsed by cd-hit-est. We chose to use this target, rather than the TransDecoder CDS files, because if there are fragmentary or non-coding RNAs that were sequenced, then some reads will correspond to those RNAs too.

cd /research/drangeli/phase2_BCG_RNAseq/Jhae_GU_trinity_assembly/
kallisto index --index=GU.Trinity.c90.kallisto.index GU.Trinity.c90.fa

In order to run Kallisto on single-end sequence, the program requires the mean and standard deviation of read lengths. The total number of reads was found using bash commands.

cd /export/groups/drangeli/morphDE/davis.3seq/filtered.reads

gunzip -c 180824/*.fastq.gz 190917/*.fastq.gz 200611/*.fastq.gz 200701/*.fastq.gz \
| sed -n -e '2~4p' \
| awk '{ print length($0); }' > read.lengths.txt

wc -l read.lengths.txt

Total read number was 1,149,235,725.

Mean and standard deviation were calculated using awk.

cat read.lengths.txt | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}} END {for (i=1;i<=NF;i++) { printf "%f %f \n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)} }'

The results:

  • mean = 84.892739 bp
  • SD = 0.507056 bp

A bash script was used to run kallisto quant for each sample and to rename the output files with the sample names. The script outputs to a folder kallisto.vs.JhaeGUtx that contains .abundance.tsv files for each sample, listing the counts for each transcript. The resulting output files were then merged into a single comma-separated values (CSV) file (309 Mb) with columns for each sample, using a custom R script.

Differential gene expression analysis

Gene expression differences were examined using the Bioconductor package DESeq2 version 1.32.0 (Love et al. 2014) in R version 4.1.3 (R Core Team 2021). The function DESeq fits a generalized linear model where counts are modeled using a negative binomial distribution with a gene-specific dispersion parameter. Means were estimated using approximate posterior estimation for generalized linear models (Zhu et al. 2018). We extracted log2 fold-change and p-values corrected by independent hypothesis weighing (Ignatiadis et al. 2016) and applied a critical threshold of 0.05. Contrasts were made for sex, wing morph and food regime, after accounting for batch effects (multiple sequencing runs). Data were analyzed separately for each stage (fifth instar juveniles and nascent adults) and for each tissue (thorax and gonads). Differential gene expression was visualized by customized plots generated using ggplot2. Variance stabilizing transformation, using the function vst, was applied before ordination using principle component analysis. Hierarchical clustering by k-means and single-linkage was examined (Fig. S4) using the pheatmap R package (Kolde 2019).

Code used in model building can be found in the R script analysis.dge.R

Fig. S4

Hierarchical clustering heatmap of samples using k-means (k=16, vertical) and single-linkage (horizontal). Population, food regime, morph, stage, sex and tissue are color-coded by bars across the top. Abbreviations: populations: AC, Aurora, Colorado; FR, Frederick, Maryland; KL, Key Largo, Florida; PK, Plantation Key, Florida; morph: LW, long-winged; SW, short-winged; stage: L5, fifth instar; sex: f, female; m, male.

Fig. S5

Volcano plots, showing log2 fold-change (LFC) and -log10 FDR-adjusted p-values from models of gene expression in the adult gonads based on correlation to morph (A-C), wing shape PC1 (D-F), and thorax shape PC1 (G). Greater log-fold change is associated with long-wing morphs (A-C), long-wing shapes (D-F), or wider thorax shapes (G). Genes are highlighted in red if they have an absolute LFC value > 1 (two-fold difference) and an FDR-adjusted p-value < 0.05.

Fig. S6

Volcano plots, showing log2 fold-change (LFC) and -log10 FDR-adjusted p-values from models of gene expression in the juvenile thorax (A,E), adult thorax (B,F), juvenile abdomen (C,G) and adult gonads (D,H) based on correlation to food regime (A-D) and continuous food density (E-H). Greater log-fold change is associated with higher food availability. Genes are highlighted in red if they have an absolute LFC value > 1 (two-fold difference) and an FDR-adjusted p-value < 0.05. Transcripts associated with transposons are labeled “r.t.”.

Code used to generate plots of normalized expression for genes-of-interest can be found in the R script genes.of.interest.R

Fig. S7

Gene expression by morph for select transcription factors: schnurri (A-D), Mohawk (E-H), castor (I-L) and Sox14 (M-N) in the adult thorax (A,E,I), gonads (B,F,J,M), ovaries (C,G,K,N) and testes (D,H,L). Expression is given as read counts normalized for library size in each tissue dataset. For thorax and gonads (combining females and males) counts are seperated by morph and sex. Within panels, points represent normalized counts for each sample. The distribution is summarized by a density-based violin plot and by a box plot bounded at the upper and lower quartiles with a crossbar at the median. Expression differences between morphs were tested for ther data in each panel using Welsh’s t-test with FDR-correction for multiple tests. P-values < 0.05 are shown in the title of panels where they apply. Sox14 expression did not pass the minimum count cutoff for analysis in the thorax and testes.

Fig. S8

Gene expression by morph for insulin signaling pathway components: InR2 (A-D), Akt (E-H) and FoxO (I-L) in the adult thorax, gonads, ovaries and testes. Expression is given as read counts normalized for library size in each tissue dataset. For thorax and gonads (combining females and males) counts are seperated by morph and sex. Within panels, points represent normalized counts for each sample. The distribution is summarized by a density-based violin plot and by a box plot bounded at the upper and lower quartiles with a crossbar at the median. Expression differences between morphs were tested for ther data in each panel using Welsh’s t-test with FDR-correction for multiple tests. P-values < 0.05 are shown in the title of panels where they apply. InR1 expression did not pass the minimum count cutoff for analysis in any of the sampled tissues.

Fig. S9

Gene expression by morph for genes related to the TOR signaling pathway: slimfast (A-D), rheb (E-H), charybde (I-L), TOR (M-P) and S6K (Q-T) in the adult thorax, gonads, ovaries and testes. Expression is given as read counts normalized for library size in each tissue dataset. For thorax and gonads (combining females and males) counts are seperated by morph and sex. Within panels, points represent normalized counts for each sample. The distribution is summarized by a density-based violin plot and by a box plot bounded at the upper and lower quartiles with a crossbar at the median. Expression differences between morphs were tested for ther data in each panel using Welsh’s t-test with FDR-correction for multiple tests. P-values < 0.05 are shown in the title of panels where they apply.

Enrichment analysis

Enrichment analyses were performed for differentially expressed genes from each model based on annotations with terms from the GO and KEGG ontologies, as well as EggNOG protein domains, applied to transcripts by EnTAP. Genes significant positive and negative expression bias were analyzed separately. We also tested for enrichment of xenic or contaminant transcripts among those that were differentially expressed, and neither of these categories was significantly over-represented. For each term, p-values from the hypergeometric test, implemented in the base R function phyper, were adjusted for false discovery rates (FDR). Descriptions of GO terms were obtained using the R package GO.db (Carlson 2021). Names of KEGG pathways can be obtained from the KEGG website via, e.g. curl http://togows.dbcls.jp/entry/pathway/map04974/name. This call was automated using the R function RCurl::getURL (Temple Lang 2022). Terms from GO and KEGG ontologies and EggNOG protein domains over-represented in differentially expressed genes in each dataset and contrast are listed in Table S6.

For more details on the enrichment analysis see the R script enrichment.R

Table S6 Enriched annotation terms.

Note that lipid-binding proteins, such as apolipoprotein E4, have human alleles associated with increased risk of neurodegenerative diseases, such as Alzheimer disease, explaining the appearance of disease-related annotation terms here.

stage tissue model bias ontology enriched terms descriptions of top terms (adjusted p-values from HGT)
juvenile thorax sex female GO 0
juvenile thorax sex female KEGG 0
juvenile thorax sex female eggNOG 11 DM, 3e-04; Apis_Csd, 0.0081; CD34_antigen, 0.0081; DFDF, 0.0081; FDF, 0.0081; FFD_TFG, 0.0081; SDP_N, 0.0081; BAT2_N, 0.014; Btz, 0.019; MOZ_SAS, 0.023
juvenile thorax sex male GO 0
juvenile thorax sex male KEGG 0
juvenile thorax sex male eggNOG 7 CDC48_2, 0.0051; CDC48_N, 0.0051; DM, 0.0051; Meckelin, 0.0051; Vps4_C, 0.016; AAA_2, 0.03; RuvB_N, 0.035
adult thorax sex female GO 479 GO:0022626 cytosolic ribosome, 1.2e-45; GO:0006412 translation, 4.9e-43; GO:0010467 gene expression, 9.3e-34; GO:0005622 intracellular anatomical structure, 1.9e-33; GO:0043228 non-membrane-bounded organelle, 2e-30; GO:0043232 intracellular non-membrane-bounded organelle, 2e-30; GO:0044391 ribosomal subunit, 2e-30; GO:0000022 mitotic spindle elongation, 8e-30; GO:0051231 spindle elongation, 2.2e-29; GO:0003735 structural constituent of ribosome, 2.3e-29
adult thorax sex female KEGG 3 map04974 Protein digestion and absorption, 7.2e-07; map04972 Pancreatic secretion, 4.8e-05; map00513 Various types of N-glycan biosynthesis, 0.00071
adult thorax sex female eggNOG 30 CUB, 1.6e-05; COIL, 1.9e-05; LPD_N, 6.9e-05; Vitellogenin_N, 6.9e-05; Trypsin, 9.8e-05; RRM, 0.00015; RRM_1, 0.00015; Tryp_SPc, 0.00016; SIGNAL, 0.00023; DUF1943, 0.00023
adult thorax sex male GO 31 GO:0034061 DNA polymerase activity, 1.1e-14; GO:0003964 RNA-directed DNA polymerase activity, 5.1e-14; GO:0006260 DNA replication, 5.1e-14; GO:0006278 RNA-dependent DNA biosynthetic process, 5.1e-14; GO:0016779 nucleotidyltransferase activity, 2.2e-13; GO:0004523 RNA-DNA hybrid ribonuclease activity, 2e-10; GO:0006259 DNA metabolic process, 4.6e-10; GO:0004521 endoribonuclease activity, 5.3e-10; GO:0016891 endoribonuclease activity, producing 5’-phosphomonoesters, 6.8e-10; GO:0016893 endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5’-phosphomonoesters, 7.6e-10
adult thorax sex male KEGG 0
adult thorax sex male eggNOG 7 RVT_1, 8.7e-14; Exo_endo_phos, 9.5e-11; RnaseH, 1.9e-08; ZnF_C2HC, 4.1e-08; rve, 0.0035; zf-CCHC, 0.0051; DUF1891, 0.0053
juvenile gonad sex female GO 1043 GO:0005737 cytoplasm, 1.2e-59; GO:0005622 intracellular anatomical structure, 5.1e-59; GO:0043229 intracellular organelle, 4.5e-51; GO:0044237 cellular metabolic process, 8.1e-41; GO:0071704 organic substance metabolic process, 1.8e-36; GO:0044238 primary metabolic process, 6.6e-36; GO:0043228 non-membrane-bounded organelle, 8.7e-32; GO:0043232 intracellular non-membrane-bounded organelle, 8.7e-32; GO:0048856 anatomical structure development, 9.8e-32; GO:0016043 cellular component organization, 1.6e-31
juvenile gonad sex female KEGG 18 map01100 Metabolic pathways, 1.1e-10; map05012 Parkinson disease, 2.6e-06; map05010 Alzheimer disease, 2.6e-05; map05152 Tuberculosis, 0.0031; map01110 Biosynthesis of secondary metabolites, 0.0049; map04310 Wnt signaling pathway, 0.0049; map04972 Pancreatic secretion, 0.0049; map04144 Endocytosis, 0.0049; map00051 Fructose and mannose metabolism, 0.018; map05169 Epstein-Barr virus infection, 0.018
juvenile gonad sex female eggNOG 16 TRANS, 3.7e-28; SIGNAL, 1.4e-25; COIL, 9.7e-25; Miro, 7e-04; Arf, 0.0011; Ras, 0.0014; EFh, 0.0016; FN3, 0.0032; GTP_EFTU, 0.0032; fn3, 0.0036
juvenile gonad sex male GO 583 GO:0005622 intracellular anatomical structure, 8.2e-26; GO:0043229 intracellular organelle, 2.2e-22; GO:0043231 intracellular membrane-bounded organelle, 1.2e-19; GO:0043227 membrane-bounded organelle, 1.9e-19; GO:0015630 microtubule cytoskeleton, 2.1e-19; GO:0005856 cytoskeleton, 2.8e-16; GO:0016043 cellular component organization, 5.9e-15; GO:0005634 nucleus, 3e-14; GO:0043167 ion binding, 5.4e-14; GO:0048869 cellular developmental process, 5e-13
juvenile gonad sex male KEGG 15 map00710 Carbon fixation in photosynthetic organisms, 0.00091; map01100 Metabolic pathways, 0.0077; map01110 Biosynthesis of secondary metabolites, 0.0077; map04340 Hedgehog signaling pathway, 0.0077; map05110 Vibrio cholerae infection, 0.0077; map05012 Parkinson disease, 0.0097; map00480 Glutathione metabolism, 0.015; map04966 Collecting duct acid secretion, 0.016; map00030 Pentose phosphate pathway, 0.017; map05010 Alzheimer disease, 0.017
juvenile gonad sex male eggNOG 32 COIL, 2.1e-18; S_TKc, 8.2e-06; LRR, 6.8e-05; cNMP_binding, 0.001; Pkinase_Tyr, 0.001; Pkinase, 0.0013; cNMP, 0.0016; RING, 0.0017; S_TK_X, 0.0017; LRR_1, 0.003
adult gonad sex female GO 43 GO:0005622 intracellular anatomical structure, 6.3e-06; GO:0005737 cytoplasm, 6.8e-06; GO:0043229 intracellular organelle, 2.4e-05; GO:0007275 multicellular organism development, 3.1e-05; GO:0016043 cellular component organization, 0.00061; GO:0048731 system development, 0.0011; GO:0048856 anatomical structure development, 0.0023; GO:0043227 membrane-bounded organelle, 0.0091; GO:0043231 intracellular membrane-bounded organelle, 0.0098; GO:0044238 primary metabolic process, 0.0098
adult gonad sex female KEGG 0
adult gonad sex female eggNOG 0
adult gonad sex male GO 0
adult gonad sex male KEGG 0
adult gonad sex male eggNOG 0
adult thorax sex + morph long wing GO 720 GO:0005739 mitochondrion, 3.3e-109; GO:0005737 cytoplasm, 5.5e-96; GO:0005622 intracellular anatomical structure, 2.8e-78; GO:0043229 intracellular organelle, 9.7e-70; GO:0043231 intracellular membrane-bounded organelle, 1.2e-59; GO:0043227 membrane-bounded organelle, 1.4e-59; GO:0005759 mitochondrial matrix, 1.6e-54; GO:0044237 cellular metabolic process, 4.7e-52; GO:0000313 organellar ribosome, 3.3e-41; GO:0005761 mitochondrial ribosome, 3.3e-41
adult thorax sex + morph long wing KEGG 15 map01100 Metabolic pathways, 4.5e-37; map05012 Parkinson disease, 1.7e-27; map05010 Alzheimer disease, 6e-23; map01110 Biosynthesis of secondary metabolites, 1.2e-13; map00640 Propanoate metabolism, 0.00026; map01120 Microbial metabolism in diverse environments, 0.00048; map04260 Cardiac muscle contraction, 0.00048; map00280 Valine, leucine and isoleucine degradation, 0.0018; map04710 Circadian rhythm, 0.0033; map01210 2-Oxocarboxylic acid metabolism, 0.0094
adult thorax sex + morph long wing eggNOG 46 COIL, 1.1e-22; TRANS, 2.9e-13; I-set, 0.0011; IGc2, 0.0012; FAD_binding_2, 0.0012; IG, 0.0024; Myosin_tail_1, 0.0024; Peptidase_M16, 0.0024; Peptidase_M16_C, 0.0024; Pkinase_Tyr, 0.0024
adult thorax sex + morph short wing GO 805 GO:0005622 intracellular anatomical structure, 3.8e-45; GO:0005737 cytoplasm, 4.8e-37; GO:0043229 intracellular organelle, 1.1e-32; GO:0043227 membrane-bounded organelle, 2e-30; GO:0043231 intracellular membrane-bounded organelle, 4e-30; GO:0006810 transport, 8.3e-27; GO:0051234 establishment of localization, 1.2e-25; GO:0071704 organic substance metabolic process, 4.6e-23; GO:0050789 regulation of biological process, 8e-23; GO:0044238 primary metabolic process, 2.1e-22
adult thorax sex + morph short wing KEGG 5 map04974 Protein digestion and absorption, 1.2e-08; map04972 Pancreatic secretion, 0.00021; map00513 Various types of N-glycan biosynthesis, 0.0012; map01100 Metabolic pathways, 0.0036; map04512 ECM-receptor interaction, 0.027
adult thorax sex + morph short wing eggNOG 39 TRANS, 2.7e-32; SIGNAL, 2.6e-22; COIL, 2.8e-19; CUB, 1.9e-07; Allatostatin, 6e-04; Tryp_SPc, 6e-04; Trypsin, 0.00091; AIG1, 0.0035; Gtr1_RagA, 0.0036; EGF, 0.018
adult gonad sex + morph long wing GO 185 GO:0001705 ectoderm formation, 0.014; GO:0001712 ectodermal cell fate commitment, 0.014; GO:0001715 ectodermal cell fate specification, 0.014; GO:0004016 adenylate cyclase activity, 0.014; GO:0006171 cAMP biosynthetic process, 0.014; GO:0007501 mesodermal cell fate specification, 0.014; GO:0010668 ectodermal cell differentiation, 0.014; GO:0018130 heterocycle biosynthetic process, 0.014; GO:0019438 aromatic compound biosynthetic process, 0.014; GO:0034654 nucleobase-containing compound biosynthetic process, 0.014
adult gonad sex + morph long wing KEGG 25 map04020 Calcium signaling pathway, 0.0042; map04062 Chemokine signaling pathway, 0.0042; map04540 Gap junction, 0.0042; map04713 Circadian entrainment, 0.0042; map04723 Retrograde endocannabinoid signaling, 0.0042; map04724 Glutamatergic synapse, 0.0042; map04725 Cholinergic synapse, 0.0042; map04727 GABAergic synapse, 0.0042; map04911 Insulin secretion, 0.0042; map04912 GnRH signaling pathway, 0.0042
adult gonad sex + morph long wing eggNOG 5 COIL, 0.0021; CYCc, 0.0021; Guanylate_cyc, 0.0021; IPT, 0.0021; RHD, 0.0021
adult gonad sex + morph short wing GO 193 GO:0022611 dormancy process, 0.003; GO:0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity, 0.003; GO:0048169 regulation of long-term neuronal synaptic plasticity, 0.003; GO:0051823 regulation of synapse structural plasticity, 0.003; GO:0052813 phosphatidylinositol bisphosphate kinase activity, 0.003; GO:0055115 entry into diapause, 0.003; GO:0060074 synapse maturation, 0.003; GO:0001727 lipid kinase activity, 0.0046; GO:0016303 1-phosphatidylinositol-3-kinase activity, 0.0046; GO:0005942 phosphatidylinositol 3-kinase complex, 0.0049
adult gonad sex + morph short wing KEGG 51 map04725 Cholinergic synapse, 0.0027; map04012 ErbB signaling pathway, 0.0027; map04066 HIF-1 signaling pathway, 0.0027; map04070 Phosphatidylinositol signaling system, 0.0027; map04150 mTOR signaling pathway, 0.0027; map04210 Apoptosis, 0.0027; map04370 VEGF signaling pathway, 0.0027; map04380 Osteoclast differentiation, 0.0027; map04620 Toll-like receptor signaling pathway, 0.0027; map04630 JAK-STAT signaling pathway, 0.0027
adult gonad sex + morph short wing eggNOG 6 PI3K_C2, 0.00025; PI3K_p85B, 0.00025; PI3K_rbd, 0.00025; PI3Ka, 0.00025; PI3_PI4_kinase, 0.00049; PI3Kc, 0.00049
adult ovaries sex + morph long wing GO 45 GO:0005819 spindle, 0.021; GO:0005874 microtubule, 0.021; GO:0007552 metamorphosis, 0.021; GO:0005815 microtubule organizing center, 0.026; GO:0004016 adenylate cyclase activity, 0.03; GO:0006171 cAMP biosynthetic process, 0.03; GO:0008301 DNA binding, bending, 0.03; GO:0043229 intracellular organelle, 0.03; GO:0046058 cAMP metabolic process, 0.03; GO:0005622 intracellular anatomical structure, 0.042
adult ovaries sex + morph long wing KEGG 28 map04020 Calcium signaling pathway, 0.011; map04062 Chemokine signaling pathway, 0.011; map04145 Phagosome, 0.011; map04540 Gap junction, 0.011; map04612 Antigen processing and presentation, 0.011; map04713 Circadian entrainment, 0.011; map04723 Retrograde endocannabinoid signaling, 0.011; map04724 Glutamatergic synapse, 0.011; map04725 Cholinergic synapse, 0.011; map04727 GABAergic synapse, 0.011
adult ovaries sex + morph long wing eggNOG 9 CYCc, 0.0052; Guanylate_cyc, 0.0052; Inhibitor_I29, 0.0052; NUDE_C, 0.0052; Pept_C1, 0.0052; Peptidase_C1, 0.0052; Peptidase_C1_2, 0.0052; HMG, 0.0091; HMG_box, 0.0091
adult ovaries sex + morph short wing GO 56 GO:0010466 negative regulation of peptidase activity, 0.0022; GO:0030414 peptidase inhibitor activity, 0.0022; GO:0051346 negative regulation of hydrolase activity, 0.0022; GO:0061134 peptidase regulator activity, 0.0022; GO:0004857 enzyme inhibitor activity, 0.0023; GO:0052547 regulation of peptidase activity, 0.0023; GO:0043086 negative regulation of catalytic activity, 0.0053; GO:0044092 negative regulation of molecular function, 0.0059; GO:0001540 amyloid-beta binding, 0.0062; GO:0005540 hyaluronic acid binding, 0.0062
adult ovaries sex + morph short wing KEGG 0
adult ovaries sex + morph short wing eggNOG 23 SIGNAL, 0.005; C8, 0.005; Ldl_recept_b, 0.005; LY, 0.005; Pacifastin_I, 0.005; TIL, 0.005; Far-17a_AIG1, 0.0057; VWC_def, 0.0057; VWC, 0.0059; EGF_Lam, 0.0059
adult testes sex + morph long wing GO
adult testes sex + morph long wing KEGG 0
adult testes sex + morph long wing eggNOG 0
adult testes sex + morph short wing GO
adult testes sex + morph short wing KEGG 7 map04110 Cell cycle, 0.0094; map04360 Axon guidance, 0.0094; map05130 Pathogenic Escherichia coli infection, 0.0094; map05131 Shigellosis, 0.0094; map05220 Chronic myeloid leukemia, 0.0094; map04722 Neurotrophin signaling pathway, 0.016; map05200 Pathways in cancer, 0.028
adult testes sex + morph short wing eggNOG 7 FABD, 0.0057; Mic1, 0.0057; SH2, 0.016; TyrKc, 0.016; SH3, 0.026; SH3_1, 0.026; SH3_2, 0.026
adult thorax sex + wing shape long wing GO 721 GO:0005739 mitochondrion, 2.3e-110; GO:0005737 cytoplasm, 1.8e-100; GO:0005622 intracellular anatomical structure, 1.3e-79; GO:0043229 intracellular organelle, 4.8e-69; GO:0005759 mitochondrial matrix, 2.8e-58; GO:0043231 intracellular membrane-bounded organelle, 3.2e-57; GO:0043227 membrane-bounded organelle, 3.7e-57; GO:0044237 cellular metabolic process, 5e-54; GO:0000313 organellar ribosome, 6.2e-45; GO:0005761 mitochondrial ribosome, 6.2e-45
adult thorax sex + wing shape long wing KEGG 15 map01100 Metabolic pathways, 2.8e-40; map05012 Parkinson disease, 6.4e-29; map05010 Alzheimer disease, 3.5e-24; map01110 Biosynthesis of secondary metabolites, 2.5e-15; map01120 Microbial metabolism in diverse environments, 8.1e-05; map04260 Cardiac muscle contraction, 0.00043; map00640 Propanoate metabolism, 0.00043; map04710 Circadian rhythm, 0.0037; map00280 Valine, leucine and isoleucine degradation, 0.0093; map01210 2-Oxocarboxylic acid metabolism, 0.0094
adult thorax sex + wing shape long wing eggNOG 48 COIL, 4.1e-24; TRANS, 2.1e-14; I-set, 1.2e-05; IGc2, 1.5e-05; V-set, 0.00017; ig, 0.00026; IG, 0.00026; Pkinase_Tyr, 0.00026; Pkinase, 0.00029; IG_like, 0.00031
adult thorax sex + wing shape short wing GO 687 GO:0005622 intracellular anatomical structure, 3.8e-38; GO:0005737 cytoplasm, 1.1e-36; GO:0043229 intracellular organelle, 1e-28; GO:0043227 membrane-bounded organelle, 3.5e-25; GO:0043231 intracellular membrane-bounded organelle, 6.5e-25; GO:0006810 transport, 3e-23; GO:0051234 establishment of localization, 7.3e-23; GO:0071704 organic substance metabolic process, 1.8e-19; GO:0048856 anatomical structure development, 1.1e-18; GO:0050789 regulation of biological process, 1.2e-18
adult thorax sex + wing shape short wing KEGG 4 map04974 Protein digestion and absorption, 1.3e-05; map04972 Pancreatic secretion, 0.0026; map00513 Various types of N-glycan biosynthesis, 0.019; map01100 Metabolic pathways, 0.019
adult thorax sex + wing shape short wing eggNOG 26 TRANS, 1.7e-28; COIL, 5.5e-18; SIGNAL, 5.5e-18; CUB, 4.5e-05; Gtr1_RagA, 0.00045; Miro, 0.0027; Ras, 0.0027; Tubulin_C, 0.0027; Tubulin, 0.007; Arf, 0.014
adult gonad sex + wing shape long wing GO 114 GO:0004197 cysteine-type endopeptidase activity, 0.00011; GO:0005764 lysosome, 0.00011; GO:0008219 cell death, 0.00011; GO:0035070 salivary gland histolysis, 0.00011; GO:0035071 salivary gland cell autophagic cell death, 0.00011; GO:0045169 fusome, 0.00011; GO:0048102 autophagic cell death, 0.00011; GO:0000323 lytic vacuole, 0.00012; GO:0008234 cysteine-type peptidase activity, 0.00017; GO:0007435 salivary gland morphogenesis, 0.00019
adult gonad sex + wing shape long wing KEGG 5 map04612 Antigen processing and presentation, 1.1e-06; map04145 Phagosome, 1.7e-06; map05205 Proteoglycans in cancer, 4.4e-06; map05323 Rheumatoid arthritis, 0.0041; map04142 Lysosome, 0.012
adult gonad sex + wing shape long wing eggNOG 9 Inhibitor_I29, 4.3e-07; Pept_C1, 4.3e-07; Peptidase_C1, 4.3e-07; Peptidase_C1_2, 4.3e-07; SIGNAL, 0.00084; Thiol_cytolysin, 0.0035; Lipase_2, 0.0038; Lipase, 0.0073; TRANS, 0.008
adult gonad sex + wing shape short wing GO 0
adult gonad sex + wing shape short wing KEGG 0
adult gonad sex + wing shape short wing eggNOG 10 Aa_trans, 0.043; Chitin_bind_4, 0.043; DEAD, 0.043; DEXDc, 0.043; DUF1759, 0.043; Helicase_C, 0.043; HELICc, 0.043; Peptidase_A17, 0.043; RVT_2, 0.043; Sugar_tr, 0.045
adult ovaries sex + wing shape long wing GO 41 GO:0009268 response to pH, 0.011; GO:0010269 response to selenium ion, 0.011; GO:0010447 response to acidic pH, 0.011; GO:0030682 mitigation of host defenses by symbiont, 0.011; GO:0052173 response to defenses of other organism, 0.011; GO:0052200 response to host defenses, 0.011; GO:0052572 response to host immune response, 0.011; GO:0071291 cellular response to selenium ion, 0.011; GO:0075136 response to host, 0.011; GO:0008121 ubiquinol-cytochrome-c reductase activity, 0.015
adult ovaries sex + wing shape long wing KEGG 0
adult ovaries sex + wing shape long wing eggNOG 2 Sod_Fe_C, 0.0024; Sod_Fe_N, 0.0024
adult ovaries sex + wing shape short wing GO 0
adult ovaries sex + wing shape short wing KEGG 0
adult ovaries sex + wing shape short wing eggNOG 6 MIG-14_Wnt-bd, 0.0079; Pacifastin_I, 0.016; Chitin_bind_4, 0.033; DUF1759, 0.033; Peptidase_A17, 0.033; RVT_2, 0.033
adult testes sex + wing shape long wing GO 157 GO:0000131 incipient cellular bud site, 0.029; GO:0000148 1,3-beta-D-glucan synthase complex, 0.029; GO:0000935 division septum, 0.029; GO:0001837 epithelial to mesenchymal transition, 0.029; GO:0004028 3-chloroallyl aldehyde dehydrogenase activity, 0.029; GO:0004030 aldehyde dehydrogenase [NAD(P)+] activity, 0.029; GO:0005773 vacuole, 0.029; GO:0005934 cellular bud tip, 0.029; GO:0005937 mating projection, 0.029; GO:0006068 ethanol catabolic process, 0.029
adult testes sex + wing shape long wing KEGG 0
adult testes sex + wing shape long wing eggNOG 18 Lys, 0.015; LYZ1, 0.015; Peptidase_C13, 0.015; SIGNAL, 0.015; SLT, 0.015; Thyroglobulin_1, 0.015; Transglycosylas, 0.015; TY, 0.015; LuxC, 0.02; CY, 0.022
adult testes sex + wing shape short wing GO 0
adult testes sex + wing shape short wing KEGG 0
adult testes sex + wing shape short wing eggNOG 4 DEAD, 0.021; DEXDc, 0.021; Helicase_C, 0.021; HELICc, 0.021
adult thorax sex + thorax shape wide GO 0
adult thorax sex + thorax shape wide KEGG 0
adult thorax sex + thorax shape wide eggNOG 11 SIGNAL, 0.00011; CH, 0.0036; CAMSAP_CH, 0.01; CRAL_TRIO, 0.013; JHBP, 0.013; Calponin, 0.013; Polysacc_deac_1, 0.013; SEC14, 0.013; TRANS, 0.013; CRAL_TRIO_N, 0.026
adult thorax sex + thorax shape narrow GO 0
adult thorax sex + thorax shape narrow KEGG 0
adult thorax sex + thorax shape narrow eggNOG 16 DNA_pol_B_2, 0.047; DUF1162, 0.047; DUF1986, 0.047; FYRC, 0.047; FYRN, 0.047; IR1-M, 0.047; KASH, 0.047; Neur_chan_LBD, 0.047; Neur_chan_memb, 0.047; Ran_BP1, 0.047
juvenile thorax sex + morph + food density more food GO 0
juvenile thorax sex + morph + food density more food KEGG 0
juvenile thorax sex + morph + food density more food eggNOG 6 Lipocalin, 0.0057; Lipocalin_2, 0.0057; Rad50_zn_hook, 0.0057; Triabin, 0.0057; VWC_def, 0.012; VWC, 0.013
juvenile thorax sex + morph + food density less food GO 8 GO:0003916 DNA topoisomerase activity, 0.046; GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity, 0.046; GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity, 0.046; GO:0005160 transforming growth factor beta receptor binding, 0.046; GO:0006265 DNA topological change, 0.046; GO:0016191 synaptic vesicle uncoating, 0.046; GO:0072319 vesicle uncoating, 0.046
juvenile thorax sex + morph + food density less food KEGG 0
juvenile thorax sex + morph + food density less food eggNOG 8 DUF3480, 0.0013; SARA, 0.0013; TOPEUc, 0.0013; Topoisom_I, 0.0013; Topoisom_I_N, 0.0013; FYVE, 0.013; MADF_DNA_bdg, 0.014; DnaJ, 0.02
adult thorax sex + morph + food density more food GO 10 GO:0006801 superoxide metabolic process, 0.0018; GO:0072593 reactive oxygen species metabolic process, 0.0032; GO:0005319 lipid transporter activity, 0.0043; GO:0006869 lipid transport, 0.0071; GO:0010876 lipid localization, 0.01; GO:0047396 glycosylphosphatidylinositol diacylglycerol-lyase activity, 0.015; GO:0033036 macromolecule localization, 0.024; GO:0045445 myoblast differentiation, 0.024; GO:0000083 regulation of transcription involved in G1/S transition of mitotic cell cycle, 0.031
adult thorax sex + morph + food density more food KEGG 0
adult thorax sex + morph + food density more food eggNOG 10 DUF1943, 4.1e-05; LPD_N, 4.1e-05; Sod_Cu, 4.1e-05; Vitellogenin_N, 4.1e-05; VWD, 4.6e-05; PI-PLC-X, 0.0066; SIGNAL, 0.015; Tryp_SPc, 0.035; Trypsin, 0.035; zf-C2H2, 0.036
adult thorax sex + morph + food density less food GO 0
adult thorax sex + morph + food density less food KEGG 2 map04391 Hippo signaling pathway - fly, 0.044; map04660 T cell receptor signaling pathway, 0.044
adult thorax sex + morph + food density less food eggNOG 8 6PF2K, 0.0095; KTI12, 0.0095; L27_1, 0.0095; Guanylate_kin, 0.012; GuKc, 0.012; L27, 0.012; Sulfotransfer_1, 0.012; DUF1758, 0.02
juvenile gonad sex + morph + food density more food GO 57 GO:0004044 amidophosphoribosyltransferase activity, 0.01; GO:0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0.01; GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors, 0.01; GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor, 0.01; GO:0030870 Mre11 complex, 0.01; GO:0032440 2-alkenal reductase [NAD(P)+] activity, 0.01; GO:0070548 L-glutamine aminotransferase activity, 0.01; GO:0005622 intracellular anatomical structure, 0.012; GO:0035079 polytene chromosome puffing, 0.012; GO:0035080 heat shock-mediated polytene chromosome puffing, 0.012
juvenile gonad sex + morph + food density more food KEGG 10 map04010 MAPK signaling pathway, 0.014; map04141 Protein processing in endoplasmic reticulum, 0.014; map04144 Endocytosis, 0.014; map04612 Antigen processing and presentation, 0.014; map05134 Legionellosis, 0.014; map05145 Toxoplasmosis, 0.014; map05162 Measles, 0.014; map05164 Influenza A, 0.014; map00520 Amino sugar and nucleotide sugar metabolism, 0.014; map04915 Estrogen signaling pathway, 0.015
juvenile gonad sex + morph + food density more food eggNOG 10 DWB, 0.0021; GATase_2, 0.0021; IRF-3, 0.0021; MH2, 0.0021; Rad50_zn_hook, 0.0021; SIS, 0.0021; Collagen, 0.0028; HSP70, 0.0028; MreB_Mbl, 0.0028; COIL, 0.016
juvenile gonad sex + morph + food density less food GO 34 GO:0007278 pole cell fate determination, 0.0093; GO:0019090 mitochondrial rRNA export from mitochondrion, 0.0093; GO:0019093 mitochondrial RNA localization, 0.0093; GO:0030719 P granule organization, 0.014; GO:0007277 pole cell development, 0.031; GO:0043186 P granule, 0.031; GO:0045495 pole plasm, 0.031; GO:0060293 germ plasm, 0.031; GO:0008138 protein tyrosine/serine/threonine phosphatase activity, 0.036; GO:0035770 ribonucleoprotein granule, 0.036
juvenile gonad sex + morph + food density less food KEGG 0
juvenile gonad sex + morph + food density less food eggNOG 5 SMN, 0.004; DSPc, 0.0043; PTPc_DSPc, 0.0043; TUDOR, 0.0043; Y_phosphatase, 0.0048
adult gonad sex + morph + food density more food GO 41 GO:0006590 thyroid hormone generation, 0.0086; GO:0006768 biotin metabolic process, 0.0086; GO:0008523 sodium-dependent multivitamin transmembrane transporter activity, 0.0086; GO:0015111 iodide transmembrane transporter activity, 0.0086; GO:0015705 iodide transport, 0.0086; GO:0015878 biotin transport, 0.0086; GO:0015887 pantothenate transmembrane transport, 0.0086; GO:0015939 pantothenate metabolic process, 0.0086; GO:0035461 vitamin transmembrane transport, 0.0086; GO:0042403 thyroid hormone metabolic process, 0.0086
adult gonad sex + morph + food density more food KEGG 0
adult gonad sex + morph + food density more food eggNOG 6 IF2_N, 0.0037; SSF, 0.0037; zf-C2HC, 0.0037; MOZ_SAS, 0.0042; LIM, 0.012; AT_hook, 0.024
adult gonad sex + morph + food density less food GO 4 GO:0004446 inositol-hexakisphosphate phosphatase activity, 0.0073; GO:0052826 inositol hexakisphosphate 2-phosphatase activity, 0.0073; GO:0003993 acid phosphatase activity, 0.018; GO:0052745 inositol phosphate phosphatase activity, 0.018
adult gonad sex + morph + food density less food KEGG 2 map04972 Pancreatic secretion, 0.0088; map04974 Protein digestion and absorption, 0.0088
adult gonad sex + morph + food density less food eggNOG 10 Acid_phosphat_A, 0.0029; CUB, 0.011; CwfJ_C_1, 0.011; CwfJ_C_2, 0.011; Mak10, 0.011; SIGNAL, 0.011; Tryp_SPc, 0.011; Trypsin, 0.011; Allatostatin, 0.018; zf-MYND, 0.045
juvenile ovaries sex + morph + food density more food GO 144 GO:0000491 small nucleolar ribonucleoprotein complex assembly, 0.015; GO:0000492 box C/D snoRNP assembly, 0.015; GO:0001884 pyrimidine nucleoside binding, 0.015; GO:0002134 UTP binding, 0.015; GO:0002135 CTP binding, 0.015; GO:0007008 outer mitochondrial membrane organization, 0.015; GO:0009532 plastid stroma, 0.015; GO:0009570 chloroplast stroma, 0.015; GO:0009908 flower development, 0.015; GO:0010658 striated muscle cell apoptotic process, 0.015
juvenile ovaries sex + morph + food density more food KEGG 5 map04621 NOD-like receptor signaling pathway, 0.031; map04626 Plant-pathogen interaction, 0.031; map04612 Antigen processing and presentation, 0.039; map04914 Progesterone-mediated oocyte maturation, 0.039; map04915 Estrogen signaling pathway, 0.039
juvenile ovaries sex + morph + food density more food eggNOG 2 HATPase_c, 0.0099; HSP90, 0.0099
juvenile ovaries sex + morph + food density less food GO 0
juvenile ovaries sex + morph + food density less food KEGG 1 map00520 Amino sugar and nucleotide sugar metabolism, 0.039
juvenile ovaries sex + morph + food density less food eggNOG 25 A2M, 0.0035; A2M_comp, 0.0035; A2M_N, 0.0035; A2M_N_2, 0.0035; A2M_recep, 0.0035; DMPK_coil, 0.0035; Thiol-ester_cl, 0.0035; GATase_2, 0.0045; HyaE, 0.0045; PBD, 0.0045
adult ovaries sex + morph + food density more food GO 54 GO:0005319 lipid transporter activity, 1.4e-10; GO:0006869 lipid transport, 3.3e-10; GO:0006801 superoxide metabolic process, 4.6e-10; GO:0010876 lipid localization, 2e-09; GO:0072593 reactive oxygen species metabolic process, 2e-09; GO:0071702 organic substance transport, 3.5e-05; GO:0033036 macromolecule localization, 0.00098; GO:0006810 transport, 0.0055; GO:0051234 establishment of localization, 0.006; GO:0006590 thyroid hormone generation, 0.022
adult ovaries sex + morph + food density more food KEGG 0
adult ovaries sex + morph + food density more food eggNOG 16 DUF1943, 3.3e-12; LPD_N, 3.3e-12; Vitellogenin_N, 3.3e-12; Sod_Cu, 5.6e-12; VWD, 8.9e-12; DUF3608, 0.0043; MENTAL, 0.0043; SIGNAL, 0.0043; Skp1, 0.0069; Skp1_POZ, 0.0069
adult ovaries sex + morph + food density less food GO 0
adult ovaries sex + morph + food density less food KEGG 0
adult ovaries sex + morph + food density less food eggNOG 7 Acid_phosphat_A, 0.043; Chromo, 0.043; CHROMO, 0.043; RhoGAP, 0.043; small_GTPase, 0.043; zf-MYND, 0.043; zf-UBR, 0.043
juvenile testes sex + morph + food density more food GO 0
juvenile testes sex + morph + food density more food KEGG 0
juvenile testes sex + morph + food density more food eggNOG 4 COX15-CtaA, 0.026; Mlf1IP, 0.026; N-SET, 0.026; Ssl1, 0.026
juvenile testes sex + morph + food density less food GO 0
juvenile testes sex + morph + food density less food KEGG 0
juvenile testes sex + morph + food density less food eggNOG 19 Acyl_transf_1, 0.028; Acyl_transf_3, 0.028; HELICc3, 0.028; HSA, 0.028; Jnk-SapK_ap_N, 0.028; Ketoacyl-synt_C, 0.028; NRF, 0.028; PKS_ER, 0.028; PKS_KR, 0.028; PKS_KS, 0.028
adult testes sex + morph + food density more food GO 6 GO:0007278 pole cell fate determination, 0.019; GO:0019090 mitochondrial rRNA export from mitochondrion, 0.019; GO:0019093 mitochondrial RNA localization, 0.019; GO:0030719 P granule organization, 0.019; GO:0042479 positive regulation of eye photoreceptor cell development, 0.019; GO:0045315 positive regulation of compound eye photoreceptor development, 0.019
adult testes sex + morph + food density more food KEGG 4 map04360 Axon guidance, 0.026; map04510 Focal adhesion, 0.026; map04660 T cell receptor signaling pathway, 0.026; map04810 Regulation of actin cytoskeleton, 0.026
adult testes sex + morph + food density more food eggNOG 4 PBD, 0.0082; SMN, 0.0082; RhoGAP, 0.02; TUDOR, 0.02
adult testes sex + morph + food density less food GO 1
adult testes sex + morph + food density less food KEGG 0
adult testes sex + morph + food density less food eggNOG 5 dDENN, 0.0015; DENN, 0.0015; DUF1630, 0.0015; Mlf1IP, 0.0015; uDENN, 0.0015
thorax sex + stage juvenile GO 1437 GO:0005622 intracellular anatomical structure, 7e-96; GO:0071704 organic substance metabolic process, 5.8e-94; GO:0044238 primary metabolic process, 7.2e-88; GO:0043229 intracellular organelle, 4.9e-87; GO:0044237 cellular metabolic process, 1.3e-75; GO:0043227 membrane-bounded organelle, 1.4e-64; GO:0043231 intracellular membrane-bounded organelle, 1.5e-64; GO:0005737 cytoplasm, 1.3e-63; GO:0043170 macromolecule metabolic process, 1.4e-52; GO:0006807 nitrogen compound metabolic process, 2.7e-47
thorax sex + stage juvenile KEGG 74 map01100 Metabolic pathways, 2e-28; map01110 Biosynthesis of secondary metabolites, 8.4e-10; map04145 Phagosome, 5e-08; map00500 Starch and sucrose metabolism, 1.1e-06; map00982 Drug metabolism - cytochrome P450, 8.5e-06; map00980 Metabolism of xenobiotics by cytochrome P450, 9.9e-06; map03410 Base excision repair, 1.5e-05; map03420 Nucleotide excision repair, 1.5e-05; map00053 Ascorbate and aldarate metabolism, 1.8e-05; map04972 Pancreatic secretion, 2e-05
thorax sex + stage juvenile eggNOG 64 TRANS, 4.1e-75; SIGNAL, 5.7e-56; COIL, 6.6e-40; MFS_1, 8.2e-12; RRM_1, 2.7e-10; RRM, 8.3e-10; Sugar_tr, 1.3e-09; A1_Propeptide, 7.7e-07; Chitin_bind_4, 9.5e-07; Asp, 1.1e-06
thorax sex + stage adult GO 618 GO:0005739 mitochondrion, 2.9e-24; GO:0005740 mitochondrial envelope, 7.9e-19; GO:0031966 mitochondrial membrane, 1.7e-18; GO:0005622 intracellular anatomical structure, 2.3e-18; GO:0005737 cytoplasm, 1.5e-17; GO:0048856 anatomical structure development, 1.8e-17; GO:0042302 structural constituent of cuticle, 7.9e-16; GO:0005743 mitochondrial inner membrane, 8.8e-16; GO:0019866 organelle inner membrane, 1.7e-15; GO:0031967 organelle envelope, 2.1e-15
thorax sex + stage adult KEGG 4 map01100 Metabolic pathways, 1.2e-15; map05012 Parkinson disease, 1.4e-14; map05010 Alzheimer disease, 1.9e-10; map01110 Biosynthesis of secondary metabolites, 0.0071
thorax sex + stage adult eggNOG 33 TRANS, 9.7e-45; SIGNAL, 6.2e-42; Chitin_bind_4, 8.8e-15; COIL, 8.9e-15; Sod_Cu, 0.0012; LIM, 0.0025; IG, 0.0035; CBM_14, 0.0072; ChtBD2, 0.0072; LDLa, 0.0091
ovaries sex + stage juvenile GO 5 GO:0034061 DNA polymerase activity, 4.8e-06; GO:0003964 RNA-directed DNA polymerase activity, 1.5e-05; GO:0006278 RNA-dependent DNA biosynthetic process, 1.5e-05; GO:0006260 DNA replication, 0.00014; GO:0016779 nucleotidyltransferase activity, 0.0085
ovaries sex + stage juvenile KEGG 0
ovaries sex + stage juvenile eggNOG 5 RVT_1, 5e-07; ZnF_C2HC, 0.016; Exo_endo_phos, 0.017; rve, 0.033; DUF1759, 0.038
ovaries sex + stage adult GO 190 GO:0005634 nucleus, 2.7e-19; GO:0043229 intracellular organelle, 4.3e-12; GO:0090304 nucleic acid metabolic process, 7.4e-12; GO:0043227 membrane-bounded organelle, 8.6e-12; GO:0043231 intracellular membrane-bounded organelle, 8.6e-12; GO:0005622 intracellular anatomical structure, 1.2e-11; GO:0031981 nuclear lumen, 1.3e-11; GO:1901360 organic cyclic compound metabolic process, 3.4e-11; GO:0006139 nucleobase-containing compound metabolic process, 5.3e-11; GO:0006725 cellular aromatic compound metabolic process, 5.3e-11
ovaries sex + stage adult KEGG 0
ovaries sex + stage adult eggNOG 1 COIL, 2.6e-05
testes sex + stage juvenile GO 3 GO:0035070 salivary gland histolysis, 0.034; GO:0035071 salivary gland cell autophagic cell death, 0.034; GO:0048102 autophagic cell death, 0.034
testes sex + stage juvenile KEGG 0
testes sex + stage juvenile eggNOG 0
testes sex + stage adult GO 0
testes sex + stage adult KEGG 0
testes sex + stage adult eggNOG 0

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