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) ...结构变异（Structural Variations, SVs）是驯化与育种改良性状的主要来源。本研究构建了首个鸭泛基因组，整合了5套基因组组装结果，新增约40.98 Mb的序列。结合测序深度>46.5X的高深度测序数据，该泛基因组共鉴定得到101041个结构变异，其中相当比例源自转座因子（transposable element, TE）的活动。众多锚定在基因本体或调控区域的、源自转座因子的结构变异，与驯化及育种改良性状相关联。本研究结合数量遗传学与分子实验手段，解析了源自转座因子的结构变异如何改变IGF2BP1的基因表达，并产生MITF的新型转录本，进而塑造体重与羽毛颜色性状。在IGF2BP1基因座中，该源自转座因子的结构变异对体重的影响效应在鸟类中位居首位，可解释27.61%的表型变异。本研究结果凸显了在基因组学研究中以泛基因组作为参考序列的重要性，并探究了源自转座因子的结构变异在性状形成及……中的作用。 # 鸭泛基因组揭示两类源自转座因子的结构变异在演化过程中促成体重增加与白羽表型形成 [可在Dryad数据库获取本数据集]（https://doi.org/10.5061/dryad.wwpzgmsnt） 本数据集包含源自鸭泛基因组的最终fasta与gff格式文件。如有任何疑问，欢迎随时联系我们！ ## 数据与文件结构说明 ### 包含数据集： (1) 鸭泛基因组文件 1. pan_final.fa.gz：鸭泛基因组DNA序列fasta格式文件 2. pan_final.fa.fai：pan_final.fa.gz的索引文件 3. pan_final.gff.gz：pan_final.fa.gz的基因结构注释文件 (2) 关联分析所用表型数据 4. Duck_Phenotype_Collection_F2_Population.txt：Kaya与连城白鸭杂交F2群体的表型数据集 5. 列标题与说明： BW8：8周龄体重记录值（单位：克） BW9：9周龄体重记录值（单位：克） ...