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Jung et al. BMC Genomics 2012, 13:129
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Table 2 Major orthologous chromosomes among Prunus,
Fragaria and Malus
Prunus Fragaria Malus
PC1 FC2, FC4, FC5 MCl3/MC16, MC8/MC15
PC2 FC7 (MC1, MC2)/MC7
PC3 FC6 MC9/MC 17
PC4 FC3 MC3/MC11, MC5/MC10
PC5 FC5 MC14/MC6
PC6 FC1. FC3. FC6 MC2/MC15. MC3/MC11. MC4/MC12
PC7
PC8
. , --, -
FC1, FC6
FC2
MC2/MC 15, M14/M12
MC5/MC10, MC3/MC11
The orthologous chromosomes were identified based on the result from
orthology analysis using whole genome sequences (Figure 1).
not detected when the taxon pairs were investigated
separately (Table 1). The comparison of ORs from the
two-species analyses and the comparison of ORs from
the three-species analysis are shown in Figure 2. Figure
2A shows ORs between PC2 and chromosomes of Fra-
garia and Malus, detected by separate taxon pair ana-
lyses. Figure 2B shows the same ORs shown in Figure 2A
as well as the ORs shared between all three species. 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. The fig-
ures showing ORs in the other seven Prunus chromo-
somes are shown in Additional file 1: Figure S1. The
presence of red lines and green lines in Figure 2B shows
that some ORs remain syntenic only between two spe-
cies, as expected. The comparison of Figure 2A, B also
shows additional ORs, which were not detected by the
analyses of single taxon pairs. Most notable were the
large numbers of additional ORs between Prunus and
Malus that were detected in the three-species analysis.
The additional ORs that were detected mostly resided in
chromosomes that did not display major orthologous
relationships with chromosome PC2 (Figure 2B, Table 2).
This result suggests that content and/or order of the
genes in ORs that reside on non-orthologous chromo-
somes went through more rearrangements than those in
highly orthologous regions, masking their ancestral
origins.
Comparison of orthologous regions in major orthologous
and non-orthologous chromosomes
Further characterization and comparison of ORs in ortho-
logous and non-orthologous chromosomes was performed
through an examination of the size and the syntenic quality
of the ORs that were conserved in all three species. Synte-
nic quality was defined as twice the number of matching
exons divided by the total number of exons in both seg-
ments. The percentage identity (PID) and the bit score of
the BLAT matches were also compared. Table 3 shows
that the syntenic quality is higher in ORs between major
orthologous chromosomes of Prunus and Malus (21.8%)
than those between non-orthologous chromosomes
(16.8%). The ORs from both groups however, had similar
PIDs and bit scores between BLAT matches. We did not
observe many differences in syntenic quality, PID and bit
scores between major orthologous and non-orthologous
regions in the analysis between the Prunus and Fragaria
genomes, suggesting that chromosomal regions transposed
by interchromosomal rearrangements in Malus have gone
through more changes in terms of gene content and/or
gene order, but not in terms of gene sequences. A WGD
Page 5 of 12
A. B.
Figure 2 Comparison of orthologous regions (OR) from two-species analyses and those from the three-species analysis. A. ORs
between PC2 and chromosomes of Fragaria and Mla/us, detected from two separate analyses. B. The same ORs shown in A as well as ORs that
are shared by all three species. 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 Mla/us only. Data were plotted using Circos [42].
