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Open Access Research article

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

Eudald Illa1, Daniel J Sargent2, Elena Lopez Girona2, Jill Bushakra3, Alessandro Cestaro4, Ross Crowhurst5, Massimo Pindo4, Antonio Cabrera6, Esther van der Knaap6, Amy Iezzoni7, Susan Gardiner3, Riccardo Velasco4, Pere Arús1, David Chagné3 and Michela Troggio4*

Author affiliations

1 IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348 Cabrils (Barcelona), Spain

2 East Malling Research, New Road, East Malling, Kent ME19 6BJ UK

3 The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Private Bag 11600, Palmerston North 4442, New Zealand

4 IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E Mach 1, 38010 San Michele all'Adige (TN), Italy

5 The New Zealand Institute for Plant & Food Research Limited, Mt Albert Research Centre, Private Bag 92169, Auckland 1142, New Zealand

6 Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster OH 44691, USA

7 Department of Horticulture, Michigan State University, East Lansing MI 48824, USA

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Citation and License

BMC Evolutionary Biology 2011, 11:9  doi:10.1186/1471-2148-11-9

Published: 12 January 2011

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.