Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies
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Author
Jung, Sook
Cestaro, Alessandro
Troggio, Michela
Main, Dorrie
Zheng, Ping
Cho, Ilhyung
Folta, Kevin M
Sosinski, Bryon
Abbott, Albert
Celton, Jean-Marc
Shulaev, Vladimir
Verde, Ignazio
Morgante, Michele
Rokhsar, Daniel
Velasco, Riccardo
Sargent, Daniel James
Publication date
2012-04-04ISSN
1471-2164
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
Pages
12
Publisher
BMC
Is part of
BMC Genomics
Citation
Jung, Sook, Alessandro Cestaro, Michela Troggio, Dorrie Main, Ping Zheng, Il-Hyung Cho, Kevin M. Folta, et al. 2012. “Whole Genome Comparisons of Fragaria, Prunus and Malus Reveal Different Modes of Evolution Between Rosaceous Subfamilies.” BMC Genomics 13 (1): 129. doi:10.1186/1471-2164-13-129.
Program
Genòmica i Biotecnologia
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