title: Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA. sook_jung@wsu.edu
authors.forename: Sook
authors.initials: S
authors.lastname: Jung
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
authors.forename: Ping
authors.initials: P
authors.lastname: Zheng
authors.forename: Ilhyung
authors.initials: I
authors.lastname: Cho
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Folta
authors.forename: Bryon
authors.initials: B
authors.lastname: Sosinski
authors.forename: Albert
authors.initials: A
authors.lastname: Abbott
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Celton
authors.forename: Pere
authors.initials: P
authors.lastname: Arús
authors.forename: Vladimir
authors.initials: V
authors.lastname: Shulaev
authors.forename: Ignazio
authors.initials: I
authors.lastname: Verde
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Daniel
authors.initials: D
authors.lastname: Rokhsar
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Daniel James
authors.initials: DJ
authors.lastname: Sargent
mesh_terms: D000465:Algorithms; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D031985:Fragaria / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D027845:Malus / Q000235:genetics; D010802:Phylogeny; D027861:Prunus / Q000235:genetics; D012393:Rosacea / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid