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Nine high-quality Anas genomes provide insights into Anas evolution and domestication
Zhou Zhang1, Zijia Ni2, Te Li2
1State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing 100000, China; National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang 330000, China.
Cell Reports
|April 2, 2025
Summary
Duck genomes reveal Z chromosome stability and key genetic changes during domestication. Structural variations and retrotransposon bursts accelerated duck domestication, impacting genes like MITF and IGF2BP1.
Area of Science:
- Genomics
- Evolutionary Biology
- Animal Science
Background:
- Understanding duck (Anas) species diversity and domestication processes is crucial but remains unclear.
- Previous evolutionary studies have provided insights into wild and domestic organisms, but a comprehensive analysis of duck evolution is lacking.
Purpose of the Study:
- To investigate the evolutionary history and domestication of ducks using chromosome-level genomes.
- To identify genetic factors, including structural variations and mobile elements, that contributed to duck domestication.
Main Methods:
- Assembly of eight chromosome-level Anas genomes and integration with the Pekin duck genome.
- Comparative genomic analysis focusing on autosomes and the Z chromosome.
- Construction of an Anas pan-genome to identify structural variations (SVs).
- Analysis of retrotransposon activity, specifically long terminal repeat (LTR) retrotransposons.
Main Results:
- The Z chromosome showed less introgression and more stable phylogenies compared to autosomes.
- Speciation of Anas platyrhynchos and Anas zonorhyncha involved female-biased gene flow.
- Identified differentiated SVs between domestic and wild ducks, potentially regulating genes like GHR and FER.
- A burst of LTR retrotransposons accelerated duck domestication, influencing MITF and IGF2BP1 gene functions.
Conclusions:
- The Z chromosome offers a stable perspective for understanding Anas speciation and domestication.
- Specific SVs and LTR retrotransposon activity are key drivers of duck domestication.
- This study provides a model for understanding animal evolutionary processes through genomic analysis.
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