Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints

Stephen J. Bush, Atahualpa Castillo Morales, Jaime M. Tovar-Corona, Lu Chen, Paula X. Kover, Araxi O. Urrutia

Research output: Contribution to journalArticle

17 Citations (Scopus)
92 Downloads (Pure)

Abstract

The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are over-represented amongst 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 characterised genes which 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.
Original languageEnglish
Pages (from-to)59-69
Number of pages11
JournalMolecular Biology and Evolution
Volume31
Issue number1
Early online date25 Sep 2013
DOIs
Publication statusPublished - Jan 2014

Fingerprint

genomics
gene
Genes
genes
exons
Exons
genome
Plant Genome
DNA Transposable Elements
Disease Resistance
disease resistance
alternative splicing
Alternative Splicing
Arabidopsis
transposons
gene expression
Arabidopsis thaliana
Genome
Gene Expression

Cite this

@article{c67872980324445b9884f2d823f6aecb,
title = "Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints",
abstract = "The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are over-represented amongst 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 characterised genes which 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.",
author = "Bush, {Stephen J.} and {Castillo Morales}, Atahualpa and Tovar-Corona, {Jaime M.} and Lu Chen and Kover, {Paula X.} and Urrutia, {Araxi O.}",
year = "2014",
month = "1",
doi = "10.1093/molbev/mst166",
language = "English",
volume = "31",
pages = "59--69",
journal = "Molecular Biology and Evolution",
issn = "0737-4038",
publisher = "Oxford University Press",
number = "1",

}

TY - JOUR

T1 - Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints

AU - Bush, Stephen J.

AU - Castillo Morales, Atahualpa

AU - Tovar-Corona, Jaime M.

AU - Chen, Lu

AU - Kover, Paula X.

AU - Urrutia, Araxi O.

PY - 2014/1

Y1 - 2014/1

N2 - The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are over-represented amongst 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 characterised genes which 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.

AB - The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are over-represented amongst 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 characterised genes which 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.

UR - http://www.scopus.com/inward/record.url?scp=84891821784&partnerID=8YFLogxK

UR - http://dx.doi.org/10.1093/molbev/mst166

U2 - 10.1093/molbev/mst166

DO - 10.1093/molbev/mst166

M3 - Article

VL - 31

SP - 59

EP - 69

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 1

ER -