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Open Access item Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes
|Citation:||BMC Genomics. 2006; 7: 81|
|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 pseudoancestral
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.
|Description:||This article is available from: http://www.biomedcentral.com/1471-2164/7/81|
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