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

Jung et al. BMC Genomics 2012, 13:129
http://www.biomedcentral.com/1471-2164/13/129

BGenoMC
Genomics

Whole genome comparisons of Fragaria, Prunus
and Malus reveal different modes of evolution
between Rosaceous subfamilies
Sook Jung', Alessandro Cestaro2, Michela Troggio2, Dorrie Main1, Ping Zhengi, Ilhyung Cho3, Kevin M Folta4,
Bryon Sosinski5, Albert Abbott6, Jean-Marc Celton7, Pere ArUs8, Vladimir Shulaev9, Ignazio Verde'o,
Michele Morgante", Daniel Rokhsar12, Riccardo Velasco2 and Daniel James Sargent2
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 Frogoria
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 Frogoria, Prunus and Molus 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

Background
The Rosaceae is one of the most economically important
and morphologically diverse plant families with over 90
genera containing more than 3000 species. The family
contains three sub-families; the Dryadoideae, the Rosoi-
deae and the Spireaeoideae, with the economically-
important genera Prunus and Malus contained within
the Spireaeoideae, whilst Fragaria is a member of the
* Correspondence: sook jung@wsu.edu
1Department of Horticulture and Landscape Architecture, Washington State
University, Pullman, WA 99164, USA
Full list of author information is available at the end of the article

Rosoideae [1]. The base chromosome number of the
many genera within the family ranges from x = 7 to x =
17, and recent research has suggested that the ancestral
chromosome number for Rosaceae may have been x = 9
[2,3]. As in many other plant families, comparative geno-
mics will enhance our understanding of genome struc-
ture and function and the evolutionary forces that have
led to the current chromosomal configurations of the
numerous Rosaceous species, and in turn to the mechan-
isms responsible for the wealth of morphological diver-
sity encompassed by the family. An understanding of the
degree of conservation of genome structure and function

2012 Jung et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
1 BioY ed Central Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.

Jung, Sook; Cestaro, Alessandro; Troggio, Michela; Main, Dorrie; Zheng, Ping; Cho, Ilhyung et al. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. [London, United Kingdom]. UNT Digital Library. http://digital.library.unt.edu/ark:/67531/metadc122145/. Accessed September 23, 2014.