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The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

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Abstract

We find great value in the genomes from the nonmodel organisms papaya and grape. These genomes help us understand the chromosomal history of the super-order rosids. Essential to this process are new, online genomics tools that allow researchers to easily perform their own experiments, such as identifying and evaluating syntenic regions and estimating the degree of post-tetraploidy gene fractionation (diploidization); this process is exemplified here using the online comparative genomics toolset CoGe. Using case studies, we show that two of the three genomes within the rosid paleohexaploid are more fractionated with respect to one another than to a third genome. This indicates a shared history derived from a [tetraploid]-then-[wide cross to generate a triploid]-then-[whole genome duplication to generate the hexaploid,] or similar scenario involving unreduced gametes. Two alternative hypotheses are presented that differ in terms of the mechanism and timing of fractionation.

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Acknowledgement

Funded by US National Science Foundation grant DBI0337083 to MF.

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Authors and Affiliations

  1. Department Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA

    Eric Lyons, Brent Pedersen, Josh Kane & Michael Freeling

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  1. Eric Lyons
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  2. Brent Pedersen
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  3. Josh Kane
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  4. Michael Freeling
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Correspondence to Eric Lyons.

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Lyons, E., Pedersen, B., Kane, J. et al. The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids. Tropical Plant Biol. 1, 181–190 (2008). https://doi.org/10.1007/s12042-008-9017-y

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