Sook Jung, Bryon Sosinski, Vladimir Shulaev, Alessandro Cestaro, Kevin M. Folta, Riccardo Velasco, Jean-Marc Celton, Il-Hyung Cho, Albert G. Abbott, Ping Zheng, Ignazio Verde, Michele Morgante, Michela Troggio, Daniel S. Rokhsar, Pere Arús, Dorrie Main, Daniel J. Sargent, Dept Hort & Landscape Architecture, Washington State University (WSU), Istituto Agrario di San Michele all' Adige, Univ Ctr, University Ctr, Saginaw Valley State Univ, Dept Hort Sci, University of Florida [Gainesville] (UF), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Dept Biochem & Genet, Clemson University, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ctr Recerca Agrigenom, IRTA Barcelona, Spanish National Research Council (CSIC), Dept Biol Sci, University of North Texas (UNT), CRA Fruit Tree Res Ctr, Applied Genomics Institute (IGA), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), USDA NIFA SCRI [2010-2010-03255], and University of Florida [Gainesville]
Background Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Results Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Conclusion Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae., This project has been supported by the USDA NIFA SCRI grant # 2010-2010-03255. We acknowledge International Peach Genome Initiative for the permission to use the peach genome in this study