Differentially protein expression and gene ontology term enrichment analysis
We identified 75 proteins that varied significantly between the resident and migrant juncos in early spring. Of these differentially expressed proteins (DEPs), both populations showed equal number of overexpressed proteins (Fig 4a, Table S3). The top 30 significant GO terms were extracted from the DEPs in resident and migrant juncos (FDR < 0.05). The top 5 GO annotations in each, biological process, cellular component, and molecular function, are shown in Figure 4b. The most abundant categories in biological process were nuclear-envelope organization, RNA processing, ribonucleoprotein complex biogenesis, negative regulation of cellular catabolic process, posttranscriptional regulation of gene expression, regulation of protein metabolic process, neuropeptide signaling pathway, peptide hormone processing, regulation of GTPase activity, and cell morphogenesis involved in neuron differentiation (FDR < 0.05; Figure 4b; Table S 4a).
The cellular component GO terms showed that DEPs were mainly located in cytoplasm, neuron projection cytoplasm, endomembrane system, vesicle, axon, and neuron projection (FDR < 0.05; Figure 4b; Table S 4b). The most abundant GO terms in the molecular function category were protein binding, mRNA 3-UTR binding, adrenergic receptor binding, unfolded protein binding, GTPase activator activity, enzyme regulator activity, and exopeptidase activity (Figure 4b; Table S 4c). Based on published literature search, DEPs that were also present in significant GO terms associated to reproduction (ITRP3, PURA, RP2, UCHL1, PENK, AGPAT4, GAD2, 7B2, CBE, DUSP1; Fig. 5a, Table S2), migration (SIK3, RSG7, HMGN5, DOCK7, SEPTIN 7, NCK2, STONIN 2, AIF, MCT2; Fig 5b, Table S2), and circadian clock (TARDBP, VIP, SIK3; Fig 5c, Table S2) processes were plotted as boxplot.