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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

Additional files

Additional file 3:

Table S1: List of ORs that are conserved in all three genomes with their positions and orientations in each game.

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Additional file 1:

Figure S1. Comparison of orthologous regions (OR) from two-species analysis and those from the three-species analysis. ORs between a Prunus chromosome (A:PC1, B:PC3, C:PC4, D:PC5, E:PC6, F:PC7, G:PC8) and chromosomes of Fragaria and Malus, detected from two separate analyses are shown in the diagram on the left. The same ORs shown in the diagram on the left as well as ORs that are shared by all three species are shown in the diagram on the right. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. Data with PC2 is shown in Figure 2 of the main manuscript. Data were plotted using Circos (Krzywinski et al. 2009).

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Additional file 2:

Figure S2. Orthology map identified between Prunus and the other two Rosaceous genera based on whole genome sequence analysis. The lines link one to one orthologous region identified using Mercator program (Dewey 2007). Only the orthologous regions between the major orthologous chromosomes, as shown in Table 2, are depicted. The colors represent the contiguous ancestral regions (CARs). The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. CARs that existed before the split of Prunus, Fragaria and Malus, were detected by MGRA (Multiple Genome Rearrangments and Ancestors) algorithm (Alekseyev and Pevzner 2009). A through H shows orthologous regions in Fragaria and Malus corresponding to those in Prunus chromosome 1 through 8, respectively.

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Additional file 4:

Figure S3. The chromosomes of Prunus, Fragaria, and Malus, with the colors represent the origin from the nine putative chromosomes of Rosaceae ancestor. The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. For this figure, the top 24 CARs in Figure 4 were assigned to a distinct color, depending on which of the nine chromosomes of Rosaceae ancestor they belong to. The figure was drawn using R program (Hornik 2011).

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