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doi:10.1534/genetics.106.062455
A more recent version of this article appeared on November 1, 2006.
REGULAR RESEARCH PAPERS |
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 1, Lukas A. Mueller 1, Dominique Crouzillat 2, Vincent Petiard 2 and Steven D. Tanksley 1*
1 Cornell University
2 Nestle research center, France
* To whom correspondence should be addressed. E-mail: sdt4{at}cornell.edu.
Submitted on June 23, 2006
Revised on July 31, 2006
Accepted on 8 August 2006
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 plant families -- tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidences 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.
Key Words: Universal Primers, comparative mapping, phylogenetics, single copy orthologous genes
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