The transcriptome landscapes of ovary and three oviduct segments during chicken (Gallus gallus) egg formation.

The avian embryo develops within a specialized biological container (eggshell) that contains crucial nutritional compartments (albumen, yolk). We analyzed the transcriptome of ovary and three segments of oviduct, including magnum, isthmus and uterus in the chicken during egg formation. RNA-Seq libraries (42 in total) for ovary and three different parts of the oviduct were sequenced for two different phases of egg formation. We obtained 8365 novel transcripts with an mRNA length longer than 200 bp; of these, 6832 were long intergenic non-coding RNA transcripts. We identified 547 differentially expressed genes in magnum (actively secreting albumen versus inactive) and 585 in uterus (active eggshell calcification versus quiescent). By combining QTL, transcriptome and proteome data, we obtained high quality gene lists for chicken egg formation. This is the first study to describe the ovary and oviduct transcriptomes by mRNA sequencing, and to elucidate the global repertoire of functional genes involved in egg formation.