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Geese feather production and the quality of downy feathers are additional economically important traits in the geese industry. However, little information is available about the molecular mechanisms fundamental to feather formation and the quality of feathers in geese. This study conducted de novo transcriptome sequencing analysis of two related geese species using the Illumina 4000 platform to determine the genes involved in embryonic skin feather follicle development. A total of 165,564,278 for Anser anser and 144,595,262 for Anser cygnoides clean reads were generated, which were further assembled into 77,134 unigenes with an average length of 906 base pairs in Anser anser and 66,041 unigenes with an average length of 922 base pairs in Anser cygnoides. To recognize the potential regulatory roles of differentially expressed genes (DEGs) during geese embryonic skin feather follicle development, the obtained unigenes were annotated to Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analysis. In both species, GO and KOG had shown similar distribution patterns during functional annotation except for KEGG, which showed significant variation in signaling enrichment. Anser asnser was significantly enriched in the calcium signaling pathway, whereas Anser cygnoides was significantly enriched with glycerolipid metabolism. Further analysis indicated that 14,227 gene families were conserved between the species, among which a total of 20,715 specific gene families were identified. Comparative RNA-Seq data analysis may reveal inclusive knowledge to assist in the identification of genetic regulators at a molecular level to improve feather quality production in geese and other poultry species. [ABSTRACT FROM AUTHOR]