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PMID: 15171794 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana.

BMC plant biology ·Vol. 4 ·2004-06-01 ·Pages 10

Cannon SB, Mitra A, Baumgarten A, Young ND, May G

Abstract

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. 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. 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.

MeSH Terms
Arabidopsis/genetics Arabidopsis Proteins/genetics Cysteine Endopeptidases/genetics Databases, Protein Evolution, Molecular Gene Duplication Genome, Plant Immunity, Innate/genetics Light-Harvesting Protein Complexes/genetics Multienzyme Complexes/genetics Multigene Family/genetics Phylogeny Proteasome Endopeptidase Complex Sequence Alignment/methods Tandem Repeat Sequences/genetics
Chemicals
Arabidopsis Proteins Light-Harvesting Protein Complexes Multienzyme Complexes Cysteine Endopeptidases Proteasome Endopeptidase Complex
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Cannon Steven B
Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA. [email protected]
Mitra Arvind
Baumgarten Andrew
Young Nevin D
May Georgiana
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Article Info
Journal
BMC plant biology
Abbr.
BMC Plant Biol
ISSN
1471-2229
DOI
10.1186/1471-2229-4-10
Email
[email protected]
Published
2004-06-01
Epub
2004-00-01
Pages
10
Language
English
Region
England
NLM ID
100967807
PMCID
PMC446195
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2229-4-10 PMC Full Text View journal details
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