The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana.
BACKGROUND
Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses.


RESULTS
Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions.


CONCLUSIONS
Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.
Cannon
Steven B
SB
Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA. cann0010@umn.edu
Mitra
Arvind
A
Baumgarten
Andrew
A
Young
Nevin D
ND
May
Georgiana
G
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D003546:Cysteine Endopeptidases / Q000235:genetics; D030562:Databases, Protein; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D007113:Immunity, Innate / Q000235:genetics; D045342:Light-Harvesting Protein Complexes / Q000235:genetics; D009097:Multienzyme Complexes / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D046988:Proteasome Endopeptidase Complex; D016415:Sequence Alignment / Q000379:methods; D020080:Tandem Repeat Sequences / Q000235:genetics
D029681:Arabidopsis Proteins; D045342:Light-Harvesting Protein Complexes; D009097:Multienzyme Complexes; D003546:Cysteine Endopeptidases; D046988:Proteasome Endopeptidase Complex