Why peach and grape genomes are peachy!

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Syntenic dotplot of Arabidopsis thaliana (x-axis) versus Prunus persica (Peach tree; y-axis). Analysis can be regenerated at: http://www.genomevolution.org/CoGe/SynMap.pl?dsgid1=8400;dsgid2=7043;c=4;D=40;g=20;A=5;Dm=0;gm=;w=0;b=1;ft1=1;ft2=1;ma=1;do1=1;do2=1;do=40;dt=geneorder;am=g
Syntenic dotplot of Arabidopsis thaliana (x-axis) versus Vitis viniera (grape; y-axis). Analysis can be regenerated at: http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=9048;dsgid2=7043;c=4;D=40;g=20;A=5;Dm=;gm=;w=2000;b=1;ft1=1;ft2=1;do1=1;do2=1;do=40;dt=geneorder;am=gy-axis).

Please note: This genome is currently unpublished and therefore under the publication restrictions of the Fort Lauderdale Convention.

When comparing plant genomes, it is important to understand the genomic evolutionary history of the genomes being studied. Plant genomes are relatively unique from other major groups of organisms in that their genomes undergo whole genome duplication events relatively frequently. Their evolutionary history is littered by these events, and understanding the number of shared and distinct whole genome duplication events in a plant lineage is necessary for understanding the large scale differences in genome structure observed between two plant genomes.

To the best of our knowledge, prior to the radiation of the eudicots there was a paleohexaploidy event. In other words, all eudicot genomes are derived from a common hexaploid anestor. Some of these linegaes has additional whole genome diplication events (e.g. Arbidopsis), while others have not. These genomes without subsequent whole genome duplication events since the paleohexaploidy are important to identify and place in the eudicot phylogeny as they are excellent comparator genomes for studying plant genomes with subsequent whole genome duplication events. Grape was the first genome in which the paleohexaploidy was detected. This event was easily discernible because its genome has not had a subsequent whole genome duplication event and it was easy to detect that each region of the grape genome was syntenic to two other intragenomic regions.

The release of a high-quality draft version of the peach genome by the International Peach genome Initiative] provides another wonderful addition for plant comparative genomics. Like grape, its genome hasn't had a subsequent whole genome duplication event. However, grape is a basal eurosid while peach is in the eurosid family Rosaceae (group eurosid I/Fabidae). As such, peach provides a great comparative genome for many eurosid lineages with additional whole genome duplication events.

The syntenic dotplot shown here compare:

  • grape to Arabidopsis thaliana
  • peach to Arabidopsis thaliana

This highlights that while both grape and peach can be used to show that Arabidopsis thaliana has had two subsequent whole genome duplication events since the paleohexaploidy event, the overall genomic structure between peach and Arabidopsis is more similar than that of grape to Arabidopsis. This is seen by the larger contiguous syntenic regions in the peach-Arabidopsis comparison than in the grape-Arabidopsis comparison.