Phenological transcriptomic profile of double-crested cormorants during embryonic development

In this study, we tracked the phenology of the transcriptome during double-crested cormorant (Nannopterum auritum) embryogenesis. Fresh eggs were collected from a reference site and artificially incubated from collection until four days prior to hatching. Embryos were periodically sampled throughout incubation for a total of seven time points. A custom microarray was designed for cormorants (over 14,000 probes) and used for transcriptome analysis in whole body (days 5, 8) and liver tissue (days 12, 14, 16, 20, 24). Three main development periods (early, mid, and late incubation) were identified with differentially expressed genes, gene sets, and pathways within and between each developmental transition. During artificial incubation without any exposure, whole body embryos were sampled on days 5 and 8, and the liver was samples from embryos on days 12,14,16,20,24 with n= 3-5 per sampling day. The genetic signature for each sampling day was compared to the previous and next sampling day to create a profile over time.