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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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The above 82 syntenic blocks of wheat and brachy-
podium varied in size ranging from 318 kb to 58 Mb
on corresponding brachypodium chromosomes. Two
most dense syntenic block contained 32 and 34 wESTs
that respectively spanned WC2L, 0.49
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0.50 (1% of
the arm) and WC5L, 0.55
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0.57 (2% of the arm) on
wheat chromosomes, with orthologous counterparts
on 10.9 Mb and 9.0 Mb regions of Bd5 and Bd4,
respectively (Figure 1 and Supplementary Table 3).
As we noted above, three wheat chromosomes were
highly syntenic and colinear with three brachypodium
chromosomes along their entire lengths indicating
that these three chromosomes from each genome
maintained their colinearity along large syntenic
blocks over a long evolutionary period of time
(Larkin et al., 2009). Beside this, segmental colinearity
of individual wheat chromosomes each with two
brachypodium chromosomes i.e. WC1 = Bd2/Bd3,
WC2 = Bd5/Bd1, WC5 = Bd4/Bd1 and WC7 =
Bd1/Bd3 suggested that these chromosomes might
have evolved by a number of chromosomal rearrange-
ments like breakage, translocation, fusion, etc. (Luo
et al., 2009; Qi et al., 2010). More recently, 59
syntenic blocks between brachypodium, rice, sorghum,
barley and wheat were also identified (International
Brachypodium
Initiative, 2010). These syntenic blocks
provide a genome-wide framework for understanding
the genomic rearrangements, which may be responsible
for the evolution of wheat and brachypodium genomes
during speciation.
1.5 Divergence between wheat-brachypodium ho-
mologs
Using 153 ESTs (coding sequences) that were
positioned on wheat chromosome and were syntenous
with brachypodium genome sequences, the ratios of
nonsynonymous and synonymous substitutions (Ka/Ks)
could be worked out (Supplementary Table 4). We
know that a Ka/Ks ratio less than one (<1) indicates
purifying selection (also known as negative selection
or selective constraint) and Ka/Ks ratio >1 indicates
positive selection (also known as adaptive selection or
relaxed constraint). Out of 153 ESTs, a majority of
sequence pairs (98) had Ka/Ks ratio <1, and mostly in
the range of 0.4
-
0.8 (Figure 2), suggesting that these
evolved under purifying selection that did not alter the
encoded amino acid sequence during speciation period
of 35
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40 million years (Huo et al., 2009; International
Brachypodium
Initiative, 2010). We also identified 55
fast evolving sequences with Ka/Ks ratio >1 (Figure 2).
These sequences are related to several molecular
functions, including transcription factors, binding
proteins, transport related-protein, fertility restoration
protein, cold-induced protein, disease resistance protein,
metal stress related protein, etc. Therefore, these ESTs
may be useful for identifying genes that perhaps
evolved in response to positive selection and might be
responsible for speciation in the Triticeae lineage.
Figure 2 Histogram showing Ka/Ks distribution among 153
homolog pairs of wheat and brachypodium
1.6 Comparison of wheat and brachypodium geno-
mes in relation to the intermediate ancestral genome
DNA marker data of several grass species and genome
sequence data from the following five grass species,
rice (Rice Genome Sequencing Project, 2005), maize
(Schnable et al., 2009), sorghum (Paterson et al.,
2009), brachypodium (International
Brachypodium
Initiative, 2010) and barley (Mayer et al., 2011) are
available. Information gathered from the comparison
of the marker and sequence data suggest that all grass
genomes examined so far diverged 50
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70 Mya from a
single intermediate ancestor (
n
= 12), that was derived
from an ancestral genome with
n
= 5 (Moore et al.,
1995a, b; Kellogg, 2001; Freeling, 2001; Wei et al.,
2007; Salse et al., 2008; Luo et al., 2009; Thiel et al.,
2009; Bolot et al., 2009; Devos, 2010; Qi et al., 2010).
The above five sequenced genomes cover three grass
sub-families and have chromosome numbers ranging
from
n
= 5 to
n
= 12. However, only rice genome has
a chromosome number (
n
= 12), equal to that of the
intermediate ancestral genome (Salse et al., 2008). It
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