Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
Data files
Nov 13, 2023 version files 380.71 MB
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Duck_Phenotype_Collection_F2_Population.txt
20.63 KB
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pan_final.fa.fai
156.38 KB
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pan_final.fa.gz
362.99 MB
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pan_final.gff.gz
17.55 MB
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README.md
1.51 KB
Abstract
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 livestock breeding.
[Access this dataset on Dryad] (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
- pan_final.fa.gz: duck pan-genome DNA fasta file.
- pan_final.fa.fai: index for pan_final.fa.gz
- pan_final.gff.gz: gene structure annotation for pan_final.fa.gz
(2) Phenotype data used in association analysis - Duck_Phenotype_Collection_F2_Population.txt: Phenotype dataset of Kaya x Liancheng white F2 population.
- 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)
BWHR: bodyweight of feather removed at slaughter (unit:g)
EW: evisceration weight (unit:g)
SEW: semi-evisceration weight (unit:g)
LW1: leg weight (unit:g)
BMW: breast muscle weight (unit:g)
CW: carcass weight (unit:g)
Source article
Detailed information about the shared dataset was described in the published article.
"Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution", published in iMETA 2023.