ArticleBMC evolutionary biology2012
Variation of presence/absence genes among Arabidopsis populations.
Article in BMC evolutionary biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Banana breeding by genome design.Journal of integrative plant biology · 2025Review
- Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice.Nature communications · 2023Article
- Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection.BMC genomics · 2023Article
- A pangenome analysis pipeline provides insights into functional gene identification in rice.Genome biology · 2023Article
- Accurate prediction of quantitative traits with failed SNP calls in canola and maize.Frontiers in plant science · 2023Article
- Article
- Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding.The plant genome · 2022Article
- Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.The New phytologist · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes.Frontiers in plant science · 2022Article
- QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants.G3 (Bethesda, Md.) · 2020Article
- Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus.Scientific reports · 2020Article
- Genomics of Evolutionary Novelty in Hybrids and Polyploids.Frontiers in genetics · 2020Review
- Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits.BMC genomics · 2019Article
- Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome.Plant biotechnology journal · 2019Article
- An updated gene atlas for maize reveals organ-specific and stress-induced genes.The Plant journal : for cell and molecular biology · 2019Article
- A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.PloS one · 2019Article
- Finding invisible quantitative trait loci with missing data.Plant biotechnology journal · 2018Article
- MLPA-Based Analysis of Copy Number Variation in Plant Populations.Frontiers in plant science · 2017Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene presence/absence (P/A) polymorphisms are commonly observed in plants and are important in individual adaptation and species differentiation. Detecting their abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms in a given species. The recently sequenced 80 Arabidopsis genomes provide an opportunity to address these questions.
resultsBy systematically investigating these accessions, we identified 2,407 P/A genes (or 8.9%) absent in one or more genomes, averaging 444 absent genes per accession. 50.6% of P/A genes belonged to multi-copy gene families, or 31.0% to clustered genes. However, the highest proportion of P/A genes, outnumbered in singleton genes, was observed in the regions near centromeres. In addition, a significant correlation was observed between the P/A gene frequency among the 80 accessions and the diversity level at P/A loci. Furthermore, the proportion of P/A genes was different among functional gene categories. Finally, a P/A gene tree showed a diversified population structure in the worldwide Arabidopsis accessions.
conclusionsAn estimate of P/A genes and their frequency distribution in the worldwide Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes, by which individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.
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