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-250 004, India
Author    Correspondence author
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 May, 2012
© 2012 BioPublisher Publishing Platform
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-Bd2/Bd3, WC2-Bd1/Bd5, WC3-Bd2, WC4-Bd1, WC5-Bd4/Bd1/Bd3, WC6-Bd3 and WC7-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

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). Therefore, considerable efforts and resources have been invested in developing genomic resources of brachypodium. These efforts led to the development of 20 449 ESTs (Vogel et al., 2006), two BAC libraries (Huo et al., 2006), 64 696 BAC-end sequences (Huo et al., 2008) and the high-quality genome sequence of brachypodium (International Brachypodium Initiative, 2010). Using some of the above genomic resources, comparative genomics studies revealed a closer relationship of Triticeae grasses with brachypodium relative to that with either rice or maize (Huo et al., 2009; Gu et al., 2009; Kumar et al., 2009). The phylogenetic studies involving chloroplast genome sequences of brachypodium also confirmed close relationship with other members of the tribe Triticeae (Bortiri et al., 2008). Orthologous relationships between brachypodium genome and those of rice, sorghum, barley, hexaploid wheat and Aegilops tauschii have also been observed (International Brachypodium Initiative, 2010). Besides the above, putative position of centromere in each brachypodium chromosome has been identified using conserved centromeric gene sequences (COS-C) of wheat and rice (Qi et al., 2010). Keeping in view a growing interest in the brachypodium genome as a model system for temperate grass species such as wheat, we compared the bin-mapped wheat ESTs (taken from individual wheat chromosomes) with brachypodium genome to decipher the syntenic relationships between these two species and also to relate the derived information with the known syntenic relationship between wheat and rice (La Rota and Sorrells, 2004). The results of this study are presented in this communication.

1 Results and Discussion
1.1 Matching of mapped wESTs with brachypodium genome sequences
During the present study, a total of 8 210 mapped wEST sequences distributed on all the 21 wheat chromosomes were subjected to BLASTN, each against the sequences of five brachypodium chromosomes (Bd1 to Bd5) representing 8× coverage of ~271 Mb genomic sequence of brachypodium. Using wESTs as query sequences, the number of significant hits to brachypodium chromosome sequences were found to exceed the number of non-significant hits at very high stringent conditions of BLASTN analysis that took into account not only similarity of sequences (average 90% CIP) but also relative lengths of the sequences matched (87.5% CALP). Out of 8 210 mapped wESTs, 5 208 (63.4%) ESTs showed significant hits against brachypodium chromosomes, and included 4 804 (92.3%) wESTs that were earlier mapped to specific bins of wheat chromosomes belonging to different homoeologous groups (Table 1). Remaining 404 wESTs were earlier assigned either to chromosomes or their arms only, but were not assigned defined positions involving known deletion bins.


Table 1 Genome-wide homology of 8 210 mapped wheat EST sequences with brachypodium chromosomes


Most of the 4 804 wESTs, which showed homology with brachypodium (wheat/brachypodium homologs), each had two or three homoeoloci involving homoeologous chromosomes of the concerned group; the physical order of these homoeoloci among three chromosomes was also nearly similar, irrespective of the size of individual chromosome within a homoeologous group. Therefore, based on conserved syntenic regions and extensive colinearity, the bin mapping information of each of the three homoeologs of wheat was integrated and consensus physical maps for each of the seven homoeologous groups (total 7 consensus chromosomes), namely WC1 to WC7 were generated and used for study of synteny between wheat and brachypodium genomes (see material and methods for details; Supplementary Table 1). A total of 1 380 of the 4 804 bin-mapped wESTs that gave significant hits with brachypodium chromosomes could also be assigned to the bins of wheat consensus chromosomes WC1 to WC7 (Table 1). Majority of wESTs belonging to an individual wheat consensus chromosome were shared by one or two brachypodium chromosomes. For instance, WC3, WC4 and WC6 exhibited a relatively high level of synteny with Bd2, Bd1 and Bd3, respectively. Similarly, WC1, WC2, WC5 and WC7 showed composite synteny with Bd2/Bd3, Bd5/Bd1, Bd4/Bd1 and Bd1/Bd3, respectively. The results of the present study extend the earlier work of Sorrells et al (2003) and La Rota and Sorrels (2004), where syntenic relationship between seven homoeologous groups of wheat and twelve rice chromosomes were established. Comparative analysis between the genomes of wheat and brachypodium indicate that most individual brachypodium chromosomes had homoeologs of wheat genes (ESTs) from one or more consensus chromosomes and vice-versa. These common features indicated that both the genomes evolved from a common ancestor. Regions of similarity between wheat and brachypodium genomes, studied through chromosome to chromosome matching are shown in figure 1.


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