Abstract
BackgroundGeese were domesticated over 6,000 years ago, making them one of the first domesticated poultry. Geese are capable of rapid growth, disease resistance, and high liver lipid storage capacity, and can be easily fed coarse fodder. Here, we sequence and analyze the whole-genome sequence of an economically important goose breed in China and compare it with that of terrestrial bird species.ResultsA draft sequence of the whole-goose genome was obtained by shotgun sequencing, and 16,150 protein-coding genes were predicted. Comparative genomics indicate that significant differences occur between the goose genome and that of other terrestrial bird species, particularly regarding major histocompatibility complex, Myxovirus resistance, Retinoic acid-inducible gene I, and other genes related to disease resistance in geese. In addition, analysis of transcriptome data further reveals a potential molecular mechanism involved in the susceptibility of geese to fatty liver disease and its associated symptoms, including high levels of unsaturated fatty acids and low levels of cholesterol. The results of this study show that deletion of the goose lep gene might be the result of positive selection, thus allowing the liver to adopt energy storage mechanisms for long-distance migration.ConclusionsThis is the first report describing the complete goose genome sequence and contributes to genomic resources available for studying aquatic birds. The findings in this study are useful not only for genetic breeding programs, but also for studying lipid metabolism disorders.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0652-y) contains supplementary material, which is available to authorized users.
Highlights
Geese were domesticated over 6,000 years ago, making them one of the first domesticated poultry
By combining homology-based, ab initio prediction and transcriptomeassisted methods, we predicted 16,150 genes (Additional file 1: Table S3), 75.7% of which are supported by homology-based evidence (Additional file 1: Table S4), and 77.7% are covered by transcriptome reads (Table 1)
We found that Retinoic acid-inducible gene I (RIG-I) genes aligned well between goose and zebra finch (Additional file 1: Tables S17 and S18), but only fragments of the goose RIG-I aligned with the chicken and turkey RIG-I genes (Additional file 1: Table S19)
Summary
Geese were domesticated over 6,000 years ago, making them one of the first domesticated poultry. We sequence and analyze the whole-genome sequence of an economically important goose breed in China and compare it with that of terrestrial bird species. Geese play an important role in agricultural economics, with China producing the vast majority (94%) of the approximately 2.23 million tons of goose meat consumed worldwide annually, followed by Egypt, Hungary, and Poland [1]. Compared with other terrestrial poultry (for example, chicken and turkey), waterfowl, such as ducks and geese possess uniquely favorable economic traits. They exhibit a low susceptibility to certain avian viruses, showing little or no symptoms while still acting as a virus carrier, making them a natural repository for. Lu et al Genome Biology (2015) 16:89 may serve as an important reference for the study of lipid metabolism disorders in humans
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