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

View Article: PubMed Central - PubMed

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.

No MeSH data available.


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.
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f3: 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.

Mentions: In geese, the high capability to digest fibre-rich feed is quite notable. As shown in Fig. 3A,B, ‘other glycan degradation’ was a significantly enriched KEGG pathway among both the rapidly evolving genes and the expanded gene families. As the main component of grass fibres (cellulose) is a glycan, and considering the existence of several other carbohydrate metabolism pathways (such as ‘pentose phosphate’ and ‘fructose and mannose metabolism), these results suggest that the goose genome potentially enables better digestion and absorption of this polysaccharide-based feed source. However, the composition of the gut microbiota indicates a clear pathway from cellulose to pyruvate before entering the tricarboxylic acid (TCA) cycle, as shown in Fig. 3C.


Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose
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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5016989&req=5

f3: 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.
Mentions: In geese, the high capability to digest fibre-rich feed is quite notable. As shown in Fig. 3A,B, ‘other glycan degradation’ was a significantly enriched KEGG pathway among both the rapidly evolving genes and the expanded gene families. As the main component of grass fibres (cellulose) is a glycan, and considering the existence of several other carbohydrate metabolism pathways (such as ‘pentose phosphate’ and ‘fructose and mannose metabolism), these results suggest that the goose genome potentially enables better digestion and absorption of this polysaccharide-based feed source. However, the composition of the gut microbiota indicates a clear pathway from cellulose to pyruvate before entering the tricarboxylic acid (TCA) cycle, as shown in Fig. 3C.

View Article: PubMed Central - PubMed

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.

No MeSH data available.