Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies Page: 10
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Jung et al. BMC Genomics 2012, 13:129
Page 10 of 12
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Figure 5 The Concentric circle of Rosaceae genomes. The innermost circle represents the putative nine chromosomes of Rosaceae ancestral
genome. Next sets of circles represent eight, 17 and seven chromosomes of Prunus, Ma/us and Froagria, respectively. The regions originated
from each Rosaceae ancestral chromosome are highlighted with corresponding color in Figure S3. The Data were plotted using Circos .
A through H shows orthologous regions in Frogaria and Malus
corresponding to those in Prunus chromosome 1 through 8, respectively.
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).
CARs: Contiguous ancestral regions; MGRA: Multiple genome rearrangements
and ancestors; OR: Orthologous region; PID: Percentage identity; RosCOS:
Rosaceous conserved orthologous sequences; SSR: Simple sequence repeat;
WGD: Whole genome duplication.
We thank Colin Dewey (University of Wisconsin-Madison), Max Alekseyev
(University of South Carolina), and Martin Krzywinski (Genome Sciences
Center) for their advice on using programs, Mercator, MGRA and Circos,
respectively. This project has been supported by the USDA NIFA SCRI grant
Additional file 3: Table Si: List of ORs that are conserved in all
three genomes with their positions and orientations in each game.
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).
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).
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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, article, April 4, 2012; [London, United Kingdom]. (digital.library.unt.edu/ark:/67531/metadc122145/m1/10/: accessed October 22, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.