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Open Access Highly Accessed Research article

Synteny of Prunus and other model plant species

Sook Jung1*, Derick Jiwan1, Ilhyung Cho2, Taein Lee1, Albert Abbott3, Bryon Sosinski4 and Dorrie Main1

Author Affiliations

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

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

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

4 Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA

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BMC Genomics 2009, 10:76  doi:10.1186/1471-2164-10-76

Published: 10 February 2009

Abstract

Background

Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the comparison.

Results

We found a well conserved synteny across the Prunus species – peach, plum, and apricot – and Populus using a set of homologous Prunus BACs. Conversely, we could not detect any synteny with Arabidopsis in this region. Other peach BACs also showed extensive synteny with Populus. The syntenic regions detected were up to 477 kb in Populus. Two syntenic regions between Arabidopsis and these BACs were much shorter, around 10 kb. We also found syntenic regions that are conserved between the Prunus BACs and Medicago. The array of synteny corresponded with the proposed whole genome duplication events in Populus and Medicago. Using map-anchored Prunus sequences, we detected many syntenic blocks with several gene pairs between Prunus and Populus or Arabidopsis. We observed a more complex network of synteny between Prunus-Arabidopsis, indicative of multiple genome duplication and subsequence gene loss in Arabidopsis.

Conclusion

Our result shows the striking microsynteny between the Prunus BACs and the genome of Populus and Medicago. In macrosynteny analysis, more distinct Prunus regions were syntenic to Populus than to Arabidopsis.