Rate variation among nuclear genes and the age of polyploidy in Gossypium

David S. Senchina, Ines Alvarez, Richard C. Cronn, Bao Liu, Junkang Rong, Richard D. Noyes, Andrew H. Paterson, Rod A Wing, Thea A. Wilkins, Jonathan F. Wendel

Research output: Contribution to journalArticle

211 Citations (Scopus)

Abstract

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors, and an outgroup. Substitution rates varied widely among the 48 genes, with silent and replacement substitution levels varying from 0.018 to 0.162 and from 0.000 to 0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow threefold range. Because there was no evidence of rate heterogeneity among lineages for any gene and because rates were highly correlated in independent tests, evolutionary rate is inferred to be a property of each gene or its genetic milieu rather than the clade to which it belongs. Evidence from approximately 200,000 nucleotides (40,000 per genome) suggests that polyploidy in Gossypium led to a modest enhancement in rates of nucleotide substitution. Phylogenetic analysis for each gene yielded the topology expected from organismal history, indicating an absence of gene conversion or recombination among homoeologs subsequent to allopolyploid formation. Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA.

Original languageEnglish (US)
Pages (from-to)633-643
Number of pages11
JournalMolecular Biology and Evolution
Volume20
Issue number4
DOIs
StatePublished - Apr 1 2003

Fingerprint

Gossypium
polyploidy
Polyploidy
Genes
gene
substitution
Substitution reactions
genes
allopolyploidy
cotton
Cotton
Diploidy
diploidy
Nucleotides
nucleotides
Genome
genome
Gene Conversion
gene conversion
rate

Keywords

  • Cotton
  • Evolution
  • Gossypium
  • Molecular clock
  • Polyploidy
  • Substitution rates

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

Senchina, D. S., Alvarez, I., Cronn, R. C., Liu, B., Rong, J., Noyes, R. D., ... Wendel, J. F. (2003). Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution, 20(4), 633-643. https://doi.org/10.1093/molbev/msg065

Rate variation among nuclear genes and the age of polyploidy in Gossypium. / Senchina, David S.; Alvarez, Ines; Cronn, Richard C.; Liu, Bao; Rong, Junkang; Noyes, Richard D.; Paterson, Andrew H.; Wing, Rod A; Wilkins, Thea A.; Wendel, Jonathan F.

In: Molecular Biology and Evolution, Vol. 20, No. 4, 01.04.2003, p. 633-643.

Research output: Contribution to journalArticle

Senchina, DS, Alvarez, I, Cronn, RC, Liu, B, Rong, J, Noyes, RD, Paterson, AH, Wing, RA, Wilkins, TA & Wendel, JF 2003, 'Rate variation among nuclear genes and the age of polyploidy in Gossypium', Molecular Biology and Evolution, vol. 20, no. 4, pp. 633-643. https://doi.org/10.1093/molbev/msg065
Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD et al. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution. 2003 Apr 1;20(4):633-643. https://doi.org/10.1093/molbev/msg065
Senchina, David S. ; Alvarez, Ines ; Cronn, Richard C. ; Liu, Bao ; Rong, Junkang ; Noyes, Richard D. ; Paterson, Andrew H. ; Wing, Rod A ; Wilkins, Thea A. ; Wendel, Jonathan F. / Rate variation among nuclear genes and the age of polyploidy in Gossypium. In: Molecular Biology and Evolution. 2003 ; Vol. 20, No. 4. pp. 633-643.
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