Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

Abstract

The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes.

Figure 1. Genomic comparisons between the goose and other bird species.

(A) Super tree inference for seven birds. The topology was evaluated based on the input tree bootstrap percentages. Distances are shown in millions of years. (B) Unique and homologous gene families. The numbers of unique and shared gene families are shown in each of the diagram components, and the total number of gene families for each animal is given in parentheses. (C) Demographic history of wild and domestic geese. Reconstructed population demographics of wild and domestic geese for the past 2 million years.

Figure 2. Summary of goose and chicken metagenomes.

(A) OTUs present in goose and chicken faecal samples. (B) Differences in the gut microbiota between goose and chicken according to PCoA. (C) Heat map of differences in the gut microbiota between goose and chicken at the genus level.

Figure 3. Comparison of the gene pathways of the host genome and the gut microbiota.

(A) Enriched KEGG pathways of rapidly evolving genes and gut microbiota that are differentially represented in goose and chicken. (B) Enriched KEGG pathways of expanded gene families and gut microbiota that are differentially represented in goose and chicken. (C) Integrated analysis of gene pathways between the host genome and gut microbiota.