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Comparative Study
. 2011 Jan 12:11:9.
doi: 10.1186/1471-2148-11-9.

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

Eudald Illa  1 , Daniel J Sargent, Elena Lopez Girona, Jill Bushakra, Alessandro Cestaro, Ross Crowhurst, Massimo Pindo, Antonio Cabrera, Esther van der Knaap, Amy Iezzoni, Susan Gardiner, Riccardo Velasco, Pere Arús, David Chagné, Michela Troggio
Affiliations
Comparative Study

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

Eudald Illa et al. BMC Evol Biol. .

Abstract

Background: Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence.

Results: We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae.

Conclusions: A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

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Figures

Figure 1
Figure 1
Comparative analysis of Malus and Prunus genomes. Comparison between Malus genome sequence (MC1 to MC17) and TxE Prunus reference map (PG1 to PG8). In the figure, only syntenic markers have been included.
Figure 2
Figure 2
Comparative analysis of Malus and Fragaria genomes. Comparison between Malus genome sequence (MC1 to MC17) and diploid Fragaria FV×FN reference map (FG1 to FG7). In the figure, only syntenic markers have been included.
Figure 3
Figure 3
The major syntenic relationships observed among the Fragaria, Prunus and Malus genomes. The major syntenic relationships observed among the three genomes were revealed through a comparison of 806 genetic markers. Fragaria groups (FG1-FG7) are indicated along the x-axis of the graph, Prunus groups (PG1-PG8) along the y-axis, and Malus groups are represented by boxes plotted against the two axes. Numbers within the boxes representing Malus indicate the chromosomes having syntenic relationships.
Figure 4
Figure 4
Reconstruction of a hypothetical ancestral Rosaceae genome. Syntenic regions among the genomes were elucidated from the positions of 129 orthologous markers shared by all three genomes. The hypothetical ancestral genome contains nine chromosomes numbered Ancestral 1 (A1) - A9. Sections of the chromosomes of Malus and the linkage groups of Fragaria and Prunus are coloured according to the hypothetical ancestral chromosomes. Breakpoints indicating chromosomal fusion-fission events or reciprocal translocations correspond to arrows between coloured syntenic blocks. Red arrows indicate the positions of major inversions that can be predicted based on the fusion-fission or translocations detected. Extant chromosome/linkage group lengths assume that all nine hypothetical ancestral chromosomes were of the same length.
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References

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