Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies Page: 4
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Jung et al. BMC Genomics 2012, 13:129
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Table 1 Number and length of orthologous regions (ORs) in two-genome and three genome comparisons
Orthology Analysis No. Mean No. Matching Mean Length in Kb (Prunusi Largest Length in Mb (Prunusi
OR Exons FragarialMalus) FragarialMalus)
Prunus and Fragaria 1281 17 98.8198.41NA 1.7 1.4 NA
Prunus and Malus 349 23 200.9 NA260.5 6.1 NA 7.5
*Prunus and Malus (Split into two 706 22 175.9NA222.9 5.5NA9.1
Prunus, Fragaria and Malus
*The Malus chromosomes were divided into sub-genome 1 and 2 prior to the analyses (see Materials and Methods) so that Mercator would find ORs in each
**Number includes the matching exons in two of the three genomes compared.
Malus lineage than the occurrence of multiple, yet inde-
pendent fusion events in the Prunus and Fragaria
lineages to derive the extant genome structure that is evi-
dent in the three genera today. More instances of large-
scale chromosomal fission may be a consequence of, or
related to, the WGD that occurred in Malus lineage.
Some of the rearrangements, however, may have resulted
from the potential errors during genome sequencing and
Evaluation of orthologous regions between Fragaria,
Malus and Prunus
The evolutionary relationships among the three Rosac-
eous species studied were analysed further by investigat-
ing ORs shared amongst all three genera in addition to
those detected in each taxon pair. In total 1399 regions
that were orthologous in all three genera were identified.
The list of ORs with their positions and orientations in
each genome are given in Table S1. Table S2 lists the size
of ORs and the number of exons in each genome. The
ORs contained 667 out of 855 RosCOS that have been
anchored to the peach genome and 616 of the total 1399
ORs contained anchored RosCOS markers. The list of
RosCOS markers, their anchored positions and their
matching ORs are provided in Table S3. The longest OR
in Prunus and Fragaria was OR 627 spanning 3.5 Mb in
PC8 and 1.3 Mb in FC2 with an OR in MC9. The longest
OR in Malus was 2.6 Mb in MC4 with ORs in PC6 and
FC6 (Table 1). OR 627 contained 1318 exons and 316
genes in Prunus, 998 exons and 200 genes in Fragaria,
and 92 exons and 21 genes in Malus, respectively. The
numbers of sequences in OR 627 with matches in other
genomes were 125 exons and 62 genes in Prunus, 121
exons and 57 genes in Fragaria, and 21 exons and 6
genes in Malus, respectively. Table S4 lists all the genes
and exons in OR 627 in each genome with their posi-
tions. The longest ORs in each genome and size distribu-
tions of the ORs are given in Table S5.
When multiple species are used, as in this analysis,
pairwise homology maps can be utilized to build orthol-
ogy maps for multiple species, as Mercator will find
orthologous segments even if some anchors are missing
in one of the species. The analysis thus resulted in the
detection of additional orthologous regions that were
Figure 1 Orthology map identified between three Rosaceous genera based on whole genome sequence analysis. The lines link one to
one orthologous regions, identified using Mercator program . A. Comparison between Prunus and Fragaria, B. Comparison between Prunus
and Malus. Data were plotted using Circos . Colors for plots A and B follow the same pattern based on Prunus chromosomes.
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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/m1/4/: accessed June 21, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.