Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ~40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (>46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchored in a gene body or regulatory region are linked to domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of IGF2BP1 and generate novel transcripts of MITF, shaping body weight and plumage color. In the IGF2BP1 locus, the TE-derived SV explains the largest effect on body weight among avian species (27.61% of phenotypic variation). Our findings highlight the importance of using a pan-genome as a reference in genomics studies and explore the roles of TE-derived SVs in trait formation and in livest..., , , # Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

[Access this dataset on Dryad] ([https://doi.org/10.5061/dryad.wwpzgmsnt](https://doi.org/10.5061/dryad.wwpzgmsnt))

This dataset includes the final fasta and gff files derived from the duck pan-genome. Please feel free to contact us, if u have any questions!

## Description of the data and file structure

### Datasets included:

(1) Duck pan-genome files

1. pan\_final.fa.gz: duck pan-genome DNA fasta file.
2. pan\_final.fa.fai: index for pan\_final.fa.gz
3. pan\_final.gff.gz: gene structure annotation for pan\_final.fa.gz
(2) Phenotype data used in association analysis
4. Duck\_Phenotype\_Collection\_F2\_Population.txt: Phenotype dataset of Kaya x Liancheng white F2 population.
5. Colum header and description:
BW8: Bodyweight was recorded at 8 weeks of age (unit:g)
BW9: Bodyweight was recorded at 9 weeks of age (unit:g)
...