ArticleMolecular biology and evolution2014
Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- A gene-based pangenome reveals genomic divergence and altitudinal differentiation in allotetraploid quinoa.Frontiers in plant science · 2026Article
- 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
- Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
- Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice.Nature communications · 2023Article
- Article
- Contrasting gene-level signatures of selection with reproductive fitness.Molecular ecology · 2022Article
- Calling large indels in 1047 Arabidopsis with IndelEnsembler.Nucleic acids research · 2021Article
- High-resolution mapping of Rym14TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain.Frontiers in plant science · 2021Article
- A Reference Genome Sequence for Giant Sequoia.G3 (Bethesda, Md.) · 2020Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.PLoS genetics · 2020Article
- 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
- The poplar pangenome provides insights into the evolutionary history of the genus.Communications biology · 2019Article
- Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity.Behavioural brain research · 2018Article
- Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.Plant biotechnology journal · 2018Article
- Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity.International journal of molecular sciences · 2018Review
- Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.Genetics, selection, evolution : GSE · 2018Article
- Dark period transcriptomic and metabolic profiling of two diversePlant direct · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are overrepresented among those showing structural variations, suggesting an adaptive role for gene and exon presence-absence variation (PAV). To shed light on the possible functional relevance of polymorphic coding region loss and the mechanisms driving this process, we characterized genes that have lost entire exons or their whole coding regions in 17 fully sequenced Arabidopsis thaliana accessions. We found that although a significant enrichment in genes associated with certain functional categories is observed, PAV events are largely restricted to genes with signatures of reduced essentiality: PAV genes tend to be newer additions to the genome, tissue specific, and lowly expressed. In addition, PAV genes are located in regions of lower gene density and higher transposable element density. Partial coding region PAV events were associated with only a marginal reduction in gene expression level in the affected accession and occurred in genes with higher levels of alternative splicing in the Col-0 accession. Together, these results suggest that although adaptive scenarios cannot be ruled out, PAV events can be explained without invoking them.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.