ArticleOpen biology2025
Exploration of gene presence/absence variations in
Article in Open biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- De Novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants in Pursuit of a Pangenome Reference.Molecular ecology resources · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Exploration of gene presence/absence variations inOpen biology · 2025Article
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Authors and funding
10 authors.
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Abstract
Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.
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Registered trials
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