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

Published: 12 January 2011

Additional files

Additional file 1:

Table S1, novel Prunus EST-derived markers. Table S1 lists locus names, primer sequences, and the T×E bin map positions of the 155 novel EST-derived markers mapped in this work.

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Additional file 2:

Table S2, Fragaria genetic markers. Table S2 lists the 237 genetic markers of the diploid Fragaria FV×FN reference map, along with their marker type, method of detection and the mapping bins to which they are located.

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Additional file 3:

Table S3, markers used in this work. Table S3 lists the number and type of markers used in this work. All the available markers were tested against Malus × domestica genome using GMAP and BLASTN. Syntenic markers are those that fulfilled the criteria defined for conservation of synteny in the Materials and Methods section.

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Additional file 4:

Figure S1, Prunus and Fragaria map comparison. Figure S1 shows the comparative analysis between Prunus (PG1 to PG8) and diploid Fragaria (FG1 to FG7) reference map using the Circos program. Only markers that were also present in the Malus genome sequences were included in the Fragaria-Prunus comparison.

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Additional file 5:

Figure S2, Malus and Prunus inversions in the Malus genome. Figure S2 shows the positions in the Malus genome of the inversions detected between Malus and Prunus using the complete set of 784 anchor markers in Prunus. Apple chromosomes are divided in fractions of 10 Mb. Arrows indicate the presence of a predicted inversion.

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