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Triticeae Genomics and Genetics 2012, Vol.3, No.3, 25
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37
http://tgg.sophiapublisher.com
25
A Letter Open Access
Comparative DNA Sequence Analysis Involving Wheat, Brachypodium and Rice
Genomes Using Mapped Wheat ESTs
Sachin Kumar , Harindra Singh Balyan , Pushpendra Kumar Gupta
Molecular Biology Laboratory, Department of Genetic and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
Corresponding author email:
pkgupta36@gmail.com;
Authors
Triticeae Genomics and Genetics, 2012, Vol.3, No.3 doi: 10.5376/tgg.2012.03.0003
Received: 03 Apr., 2012
Accepted: 12 Apr., 2012
Published: 07 Mar., 2012
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Kumar et al., 2012, Comparative DNA Sequence Analysis Involving Wheat, Brachypodium and Rice Genomes Using Mapped Wheat ESTs,
Triticeae
Genomics and Genetics, Vol.3, No.3 25-37 (doi: 10.5376/tgg.2012.03.0003)
Abstract
Comparative genomics is a powerful approach to transfer genomic information from a sequenced genome to closely
related species. We conducted a comparative genomics study between wheat and brachypodium genomes, using 8 210 mapped
wESTs for BLASTn against the high-quality genome sequence of brachypodium. As many as 5 208 wESTs spread over all the 21
wheat chromosomes showed significant similarity with genomic regions in all the five brachypodium chromosomes (Bd1 to Bd5).
Wheat ESTs belonging to seven homoeologous groups were also used to construct seven consensus maps (WC1 to WC7) for wheat
chromosomes. Each consensus wheat chromosome matched only one or two brachypodium chromosomes. Following are the
broad syntenic relationship that were observed between brachypodium and wheat chromosomes: WC1
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Bd2/Bd3, WC2
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Bd1/Bd5,
WC3
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Bd2, WC4
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Bd1, WC5
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Bd4/Bd1/Bd3, WC6
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Bd3 and WC7
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Bd1/Bd3. Eighty two (82) conserved syntenic blocks were also
identified between wheat and brachypodium genomes. Ka/Ks analysis was performed on 153 sequence pairs, of which 98 had Ka/Ks
ratio <1 suggesting their evolution under purifying selection involving no divergence in encoded amino acids. Results of this study
suggested that after divergence from a common ancestral genome the common syntenic features maintained between genomes of
wheat and brachypodium.
Keywords
Wheat;
Brachypodium
; ESTs; Synteny; Genome
Background
Comparative genomics has been used in several
groups of plants to study the origin and lineage on a
macro-evolutionary scale. It involves identification of
syntenic genomic regions between related species
and helps to improve our understanding about the
organization of the genomes of related species. This
approach particularly proved useful in grasses due
to the recent availability of whole-genome sequences
of rice (genome size ~430 Mb; International Rice
Genome Sequencing Project, 2005) and brachypodium
(
Brachypodium distachyon
; genome size ~300 Mb;
International
Brachypodium
Initiative, 2010) both often
used as model systems for grass species including
wheat (genome size ~16 000 Mb). This group provides
an example, where information from a well-studied
small genome can be utilized to gain knowledge about
a large genome like that of wheat (Rubin et al., 2000).
On the availability of complete rice genome sequence,
it became possible to establish syntenic relationships
between wheat and rice chromosomes using the
available wheat (
Triticum aestivum
) genomic sequences/
bin-mapped ESTs and the rice genome sequence. A
fair level of microcolinearity was also observed
between wheat and rice genomes in some of these
studies (Chantret et al., 2004; Distelfeld et al., 2004;
Schnurbusch et al., 2007), although perturbations in
microcolinearity caused by rearrangements including
inversions, deletions, duplications, etc. were also
observed (Bennetzen, 2000; Li and Gill, 2002; Bossolini
et al., 2007; Wicker et al., 2010).
Brachypodium
with a small genome is a cool season
grass and is believed to be a better model system
than rice (a sub-tropical species) for structural and
functional genomics studies among the temperate
grass genomes such as wheat, barley (
Hordeum
vulgare
), oats (
Avena sativa
), etc. (Draper et al., 2001).
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