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.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.