Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years

Michael S Barker, Nolan C. Kane, Marta Matvienko, Alexander Kozik, Richard W. Michelmore, Steven J. Knapp, Loren H. Rieseberg

Research output: Contribution to journalArticle

205 Citations (Scopus)

Abstract

Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae - a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33-38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest that paleopolyploidy can yield strikingly consistent signatures of gene retention in plant genomes despite extensive lineage radiations and recurrent genome duplications but that these patterns vary substantially among higher taxonomic categories.

Original languageEnglish (US)
Pages (from-to)2445-2455
Number of pages11
JournalMolecular Biology and Evolution
Volume25
Issue number11
DOIs
StatePublished - Nov 2008
Externally publishedYes

Fingerprint

Duplicate Genes
duplicate genes
Asteraceae
genome
gene
Genome
Expressed Sequence Tags
genes
Genes
Radiation
structural component
Plant Genome
Gene Ontology
angiosperm
Nucleic Acid Databases
expressed sequence tags
Arabidopsis
genomics
Eocene
Antarctica

Keywords

  • Asteraceae
  • Compositae
  • Duplicate gene retention
  • Genome evolution
  • Paleopolyploidy
  • Whole-genome duplication

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. / Barker, Michael S; Kane, Nolan C.; Matvienko, Marta; Kozik, Alexander; Michelmore, Richard W.; Knapp, Steven J.; Rieseberg, Loren H.

In: Molecular Biology and Evolution, Vol. 25, No. 11, 11.2008, p. 2445-2455.

Research output: Contribution to journalArticle

Barker, Michael S ; Kane, Nolan C. ; Matvienko, Marta ; Kozik, Alexander ; Michelmore, Richard W. ; Knapp, Steven J. ; Rieseberg, Loren H. / Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. In: Molecular Biology and Evolution. 2008 ; Vol. 25, No. 11. pp. 2445-2455.
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