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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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Bd3
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C-Bd3. Wheat EST BE406602 spanning the
pericentromeric region of WC6S matched a region
at 6.8 Mb in short arm of Bd3 (Qi et al., 2010),
indicating the probable position of centromere of Bd3
(Supplementary Table 1).
1.2.7 Wheat consensus chromosome 7 (WC7)
Out of 174 wESTs belonging to WC7, 56.3% were
syntenous to Bd1 (Bd1 is also largely syntenous
with WC4) and 30.5% were syntenous to Bd3. Only
13.2% wESTs were syntenous to the remaining three
brachypodium chromosomes (Bd4, Bd2 and Bd5)
(Table 1). Similar to WC2, each arm of WC7 had
segments syntenous to two brachypodium chromo-
somes. Regional homology of WC7 with Bd1 and
Bd3 suggests a possible ancestral origin and these
regions therefore precede the divergence of wheat-
brachypodium from a common ancestor. The synteny
relationship between WC7 and the brachypodium
chromosomes may be represented as follows: WC5S-
C-WC7L = Bd1/Bd3
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C-Bd3/Bd1 (Figure 1). The
relative position of Bd3 centromere could not be
deciphered, since none of the mapped wEST in
pericentromeric region of WC7 were found syntenic
to available Bd3 sequences.
Over all, there are regions of sequence similarity
and conservation that are apparent in all the wheat
chromosomes; few contain regions related to more
than one brachypodium chromosomes. Similarly, it
may also be noted that often more than one wheat
chromosomes are related to a single brachypodium
chromosome (e.g. Bd1 alone showed synteny with
entire WC4, proximal regions of WC2S and WC2L,
distal regions of WC7S and WC7L, and most
telomeric regions of WC5L). Since both the genomes
perhaps diverged independently from a single ancestor,
it is not unexpected that they have common genomic
features. The observed structural variations between
them are the consequences of sequence rearrange-
ments (genome reshuffling) during the period of
divergence.
1.3 Consensus chromosome bins containing high
density of ESTs showing homology with brachy-
podium
Due to differences in size of bins, we calculated the
expected EST density per unit bin length following
Gill et al. (1991) and Conley et al. (2004). Using these
calculated values, the ratios of the observed and
expected number of ESTs in the different bins of
individual consensus chromosomes were determined.
Out of a total of 119 bins of seven consensus wheat
chromosomes, 51 bins were such, which had higher
(1.21 to 37.91 fold) density of the observed ESTs than
the expected density of ESTs per unit fraction length
(Supplementary Table 2). Variation in the density of
genes (ESTs) along the length of the wheat
chromosomes was also reported in an earlier study (Qi
et al., 2004). Such variation has been attributed to the
following: presence of euchromatic and heterochro-
matic regions, unequal exchange of genetic material,
evolutionary history, etc. (Akhunov et al., 2003).
Further, the regions with high EST density may be
of significance in terms of gene distribution,
recombination and genome evolution among the
members of grass species (Hossain et al., 2004). These
identified regions with high EST density, which also
show synteny with brachypodium (Figure 1) was
perhaps conserved over time, and therefore, are of
evolutionary significance (Randhawa et al., 2004).
1.4 Colinear syntenic regions/blocks between wheat
and brachypodium genomes
As discussed above, the orthologous relationships
among seven consensus wheat chromosomes and five
brachypodium chromosomes suggested that most
wheat chromosomes or their bins showed homology
mainly with one or two brachypodium chromosomes,
indicating closer evolutionary relationships. Using this
relationship, a total of 82 conserved syntenic blocks
(representing 13 major blocks) between wheat and
brachypodium could be identified in the present study
(Supplementary Table 3). A conserved syntenic block
was defined, when majority of wESTs mapped in a
single bin showed colinear region on brachypodium
chromosome in a contiguous manner. Each block
comprised minimum of 3 wESTs. Within the syntenic
blocks, colinearity was recorded on the basis of their
relative best-hit order (sequence coordinates) on the
brachypodium chromosome. Few non-syntenic regions
were also observed around the syntenic blocks within
a bin, thus disrupting the colinearity between blocks.
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