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Open Access Research article

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

Sook Jung1*, Dorrie Main2, Margaret Staton1, Ilhyung Cho3, Tatyana Zhebentyayeva1, Pere Arús4 and Albert Abbott1

Author Affiliations

1 Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA

2 Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA

3 Department of Computer Science, Saginaw Valley State University, University Center, MI 48710, USA

4 Departament de Genètica Vegetal, Laboratori de Genètica Molecular Vegetal. CSIC-IRTA,08348 Cabrils, Spain

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BMC Genomics 2006, 7:81  doi:10.1186/1471-2164-7-81

Published: 14 April 2006

Abstract

Background

Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship.

Results

We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated Arabidopsis genome.

Conclusion

We report here the result of the first extensive analysis of the conserved microsynteny using DNA sequences across the Prunus genome and their Arabidopsis homologs. Our study also illustrates that both the ancestral and present Arabidopsis genomes can provide a useful resource for marker saturation and candidate gene search, as well as elucidating evolutionary relationships between species.