Different patterns of gene structure divergence following gene duplication in Arabidopsis.
BACKGROUND
Divergence in gene structure following gene duplication is not well understood. Gene duplication can occur via whole-genome duplication (WGD) and single-gene duplications including tandem, proximal and transposed duplications. Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence.


RESULTS
In Arabidopsis thaliana, we denote levels of structural divergence between duplicated genes by differences in coding-region lengths and average exon lengths, and the number of insertions/deletions (indels) and maximum indel length in their protein sequence alignment. Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure. In transposed duplications, parental loci tend to have longer coding-regions and exons, and smaller numbers of indels and maximum indel lengths than transposed loci, reflecting biased structural changes in transposed duplications. Structural divergence increases with evolutionary time for WGDs, but not transposed duplications, possibly because of biased gene losses following transposed duplications. Structural divergence has heterogeneous relationships with nucleotide substitution rates, but is consistently positively correlated with gene expression divergence. The NBS-LRR gene family shows higher-than-average levels of structural divergence.


CONCLUSIONS
Our study suggests that structural divergence between duplicated genes is greatly affected by the mechanisms of gene duplication and may be not proportional to evolutionary time, and that certain gene families are under selection on rapid evolution of gene structure.
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. paterson@plantbio.uga.edu.
Yupeng
Y
Wang
Xu
X
Tan
Andrew H
AH
Paterson
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D004251:DNA Transposable Elements / Q000235:genetics; D018628:Gene Dosage; D020440:Gene Duplication / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D005810:Multigene Family; D009711:Nucleotides / Q000235:genetics
D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D009711:Nucleotides