title: Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms.
abstract: BACKGROUND
  Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored.
  
  
  RESULTS
  In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution.
  
  
  CONCLUSIONS
  Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: Wang
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.forename: Xu
authors.initials: X
authors.lastname: Tan
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Ficklin
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D005075:Biological Evolution; D017124:Conserved Sequence; D019175:DNA Methylation; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D019684:Magnoliopsida / Q000235:genetics* / Q000502:physiology; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics; D018521:Plant Physiological Phenomena; D011401:Promoter Regions, Genetic; D012044:Regression Analysis; D017422:Sequence Analysis, DNA