Article

TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs

2025-05-26

Abstract excerpt

The genotyping of Short Interspersed Element (SINE) retrotransposon insertion polymorphisms (RIPs) from large-scale sequencing data remains technically challenging. To overcome this limitation, we developed TypeSINE to genotype SINE-RIPs from short-read sequencing data. Analyzing 362 porcine genomes, we identified 749,835 SINE-RIPs (>85% accuracy), including 65,917 common variants (5-95% frequency). These showed u...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 6f89c686-c300-54d2-926f-b1d2900ca56d
DOI: 10.1101/2025.05.21.653756

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in PigsDOI 10.1101/2025.05.21.653756Read

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigsSemantic proximity Read

Mapping and functional characterization of structural variation in 1060 pig genomes.Semantic proximity Read

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.Semantic proximity Read

A deep catalog of autosomal single nucleotide variation in the pig.Semantic proximity Read

A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.Semantic proximity Read

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption.Semantic proximity Read

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig CharacteristicsSemantic proximity Read

Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds.Semantic proximity Read

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.Semantic proximity Read

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences.Semantic proximity Read

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs.Semantic proximity Read

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data.Semantic proximity Read