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PMID: 21297981 Published · epublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift.

PloS one ·Vol. 6 ·No. 1 ·2011-01-28 ·Pages e16219

Hua Z, Zou C, Shiu SH, Vierstra RD

Abstract

The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of F-Box (FBX) genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811 FBX loci from 18 plant species, ranging from the alga Chlamydomonas reinhardtii to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of FBX loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for Carica papaya to as many as 1350 predicted for Arabidopsis lyrata. This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of FBX genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous FBX loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of FBX genes in each species. Taken together, it appears that the FBX superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid evolution potentially reflecting a central role for ubiquitylation in driving plant fitness.

MeSH Terms
Biological Evolution Evolution, Molecular F-Box Proteins/genetics Genes, Plant Genetic Drift Genetic Fitness Multigene Family Phylogeny Plants/genetics
Chemicals
F-Box Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Hua Zhihua
Department of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America.
Zou Cheng
Shiu Shin-Han
Vierstra Richard D
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0016219
Published
2011-01-28
Epub
2011-00-28
Pages
e16219
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3030570
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pone.0016219 PMC Full Text View journal details
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