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Open Access Highly Accessed Research article

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

Sook Jung1*, Alessandro Cestaro2, Michela Troggio2, Dorrie Main1, Ping Zheng1, Ilhyung Cho3, Kevin M Folta4, Bryon Sosinski5, Albert Abbott6, Jean-Marc Celton7, Pere Arús8, Vladimir Shulaev9, Ignazio Verde10, Michele Morgante11, Daniel Rokhsar12, Riccardo Velasco2 and Daniel James Sargent2

Author Affiliations

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

2 Istituto Agrario San Michele all'Adige, Via E. Mach 1, 38010 San Michele all'Adige, Italy

3 Computer Science, Saginaw Valley State University, University Center, MI 48710, USA

4 Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA

5 Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC 27695, USA

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

7 UMR Génétique et Horticulture (GenHort), INRA/Agrocampus-ouest/Université d'Angers, Centre Angers-Nantes, 42 rue Georges Morel -, BP 60057, 49071 Beaucouzé cedex, France

8 IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain

9 Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, Texas, USA

10 CRA - Fruit Tree Research Center, Via di Fioranello, 52, 00134 Rome, Italy

11 Istituto di Genomica Applicata, Parco Scientifico e Tecnologico L. Danieli, via Linussio, 51, 33100 Udine, Italy

12 DOE Joint Genomics Institute, 2800 Mitchell Dr, Walnut Creek, CA, USA

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BMC Genomics 2012, 13:129  doi:10.1186/1471-2164-13-129

Published: 4 April 2012

Abstract

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.

Keywords:
Rosaceae; Comparative genomics; Evolution