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Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.
Genetics, Vol. 174, 1407-1420, November 2006, Copyright © 2006
doi:10.1534/genetics.106.062455
Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade
Feinan Wu*,
,
Lukas A. Mueller*,,
Dominique Crouzillat
,
Vincent Pétiard and
Steven D. Tanksley*,,1
* Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, Department of Plant Biology, Cornell University, Ithaca, New York 14853 and Nestlé Research Center, 37097 Tours Cedex 2, France
1 Corresponding author: Department of Plant Breeding and Genetics, Department of Plant Biology, 248 Emerson Hall, Cornell University, Ithaca, NY 14853.
E-mail: sdt4{at}cornell.edu
We report herein the application of a set of algorithms to identify a large number (2869) of single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well as the model species Arabidopsis. Alignments of the orthologous sequences across multiple species enabled the design of "universal PCR primers," which can be used to amplify the corresponding orthologs from a broad range of taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, single-copy orthologs encode a higher-than-expected frequency of proteins transported and utilized in organelles and a paucity of proteins associated with cell walls, protein kinases, transcription factors, and signal transduction. The enabling power of this new ortholog resource was demonstrated in phylogenetic studies, as well as in comparative mapping across the plant families tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidence that (1) the ancestral species that gave rise to the core euasterid families Solanaceae and Rubiaceae had a basic chromosome number of x = 11 or 12.2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested.
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