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). 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 Materials and Methods

1.1 Sequences used for synteny analysis

A total of 8,210 wheat ESTs (wESTs) belonging to all the 21 chromosomes of wheat were downloaded from GrainGenes-SQL database (http://wheat.pw.usda.gov/cgi-bin/westsql/map_ locus_rev.cgi). The bin-map positions of these mapped ESTs were also retrieved from the same database (http://wheat.pw.usda.gov/NSF/progress_mapping.html; http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi).

A BLAST server (BrachyBlast) containing 8× sequence of five brachypodium chromosomes/pseudomolecules (build; JGI v1.0 8× 271,923,306 bp) available on-line (http://www.brachypodium.org/; http://www.brachybase.org/blast/) was used for BLAST analysis. The alignment of each mapped wEST with sequences of five different chromosomes/pseudomolecules of brachypodium was carried out by using independently each mapped wEST as a query sequence in BLAST analysis.

1.2 Criteria used for sequence comparisons

In order to simplify the analysis and to ensure the acceptable syntenic relationship between the chromosomes of wheat and brachypodium, we employed integrative sequence alignment criteria for each BLAST output with the following two parameters (Salse et al., 2008; Kumar et al., 2009): (i) Cumulative Identity Percentage (CIP) obtained using the following formula: CIP = [∑ Id of HSPs/AL] × 100, where, Id = identity; HSPs = length of high scoring segment pairs and AL = alignment length between query and subject sequences; and (ii) Cumulative Alignment Length Percentage (CALP): values of CALP were calculated as follows: CALP = [AL/QL] × 100, where, QL is the length of query sequence.

While establishing synteny between wheat and brachypodium genomes at chromosomal level, a value of 70% for CIP as well as CALP in each BLAST result was considered stringent (Salse et al., 2008). In several cases, BLAST output may often contain many HSPs due to the occurrence of redundancy or duplications in the genome. In such cases, we visually scanned the BLAST output files to determine the correct order of consecutive HSPs (in query sequence) produced by alignment between query and subject sequences (Figure 1).

1.3 Construction of consensus map of wheat genome

A map of all the seven homoeologous groups of wheat was constructed on the basis of only those wESTs that were bin-mapped to two or all the three chromosomes of a homoeologous group and also exhibited homology with sequences of brachypodium. The methodology of constructing the consensus map was described earlier in several studies (Gill et al., 1996a, b; Linkiewicz et al., 2004; Munkvold et al., 2004). On the ordered deletion bins, ESTs that detected duplicate (paralogous) loci on two or three homoeologous chromosomes were grouped according to their bin positions on each chromosome and consensus bins were defined by ESTs sharing a common mapping pattern in the same group. For example, wEST BE404868 (showing homology with brachypodium chromosome 2) mapping to the deletion bins 3AS4-0.45-1.00, 3BS1-0.33-0.57 and 3DS3-0.24-0.55, indicated a consensus bin or map position within the fraction lengths 0.45-0.55 on the short arm of group 3 chromosomes (see Supplementary Table 1). In case of non-availability or anomaly in bin-mapping information due to one of the three homoeologues, location of wEST consistent with the remaining two homoeologs was used to construct the consensus map for that individual homoeologous group. Wheat ESTs, which were earlier mapped only on one of the three homoeologous chromosomes of a group could not be placed on the consensus map, but were still utilized in the present study for improving wheat-brachypodium synteny.

1.4 Identification of centromere location

Wheat ESTs that were previously mapped to the pericentromeric regions and had homology with specific individual brachypodium chromosomes were used as query against the putative centromeres of brachypodium identified by Qi et al. (2010).

1.5 Estimation of EST density

EST density ratios were calculated by dividing the observed number of ESTs in a particular bin by the expected number of ESTs. Expected number of ESTs between the short and long arms was based on arm ratio data. The arm ratios for individual wheat chromosomes were earlier reported by Gill et al. (1991) from physical measurement of C-banded mitotic metaphase chromosomes of Chinese Spring.  

1.6 Estimation of nonsynonymous vs. synonymous substitution rates (Ka/Ks)

The sequence divergence between wheat and brachypodium matching pairs of sequences were estimated by computing the rate of nonsynonymous versus synonymous substitutions (Ka/Ks) using DnaSP v5.10 software (Librado and Rozas, 2009; http://www.ub.es/dnasp/). A total of 153 homologs, having high quality matching (85-92% CIP and CALP) were aligned using MUSCLE program in MEGA v5 software (Tamura et al., 2011) and results of the sequence alignments were saved in mega file format (.meg). These files were then analyzed for synonymous and nonsynonymous substitution rates by DnaSP v5.10.

2 Results and Discussion

2.1 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 ~271Mb 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.

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 2.

2.2 Syntenic relationship of individual wheat consensus chromosomes with brachypodium chromosomes

2.2.1 Wheat consensus chromosome 1 (WC1):

As given in Table 1, the WC1 map carries 169 matching wESTs, of which 61.5% were syntenic with Bd2 (WC3 is also largely syntenous with Bd2), 27.2% were syntenic with Bd3 and the remaining 11.3% wESTs were syntenic to the remaining three brachypodium chromosomes (Bd1, Bd4 and Bd5). The short arm of WC1 (WC1S) largely matched Bd2 except a bin between 0.48-0.50 FL (fraction length of arm) was syntenic with Bd3. The proximal region (50%) of the long arm of WC1 (WC1L) matched mainly with Bd3 and distal region (rest 50%) matched with Bd2, while the interstitial region 0.41-0.61 FL in WC1L was a composite of Bd3 and Bd2. In summary, the relationship between WC1 and brachypodium chromosomes may be summarized as follows: WC1S-C-WC1L = Bd2/Bd3/Bd2-C-Bd3/Bd2, where “C” refers to the relative position of centromere on the wheat chromosome (Figure 2). The centromere synteny between WC1, rice chromosome 5 and Bd2 is known (Qi et al., 2010). Utilizing this information wEST BE499250 in pericentromeric region of WC1S seems to be syntenic at 30.2 Mb in the short arm of Bd2 (Supplementary Table1). Therefore, this region may contain centromere of Bd2.

2.2.2 Wheat consensus chromosome 2 (WC2):

Of the 214 wESTs belonging to WC2, matched with two brachypodium chromosomes (Bd5 and Bd1). The level of similarity was higher with Bd5 (smallest chromosome) than with Bd1 (largest chromosome) as 48.6% were syntenic to Bd5 and 37.4% were syntenic to Bd1, which is largely syntenous with WC4 (Table 1; Figure 2). The remaining 14% were syntenic to the remaining three brachypodium chromosomes (Bd4, Bd2 and Bd3). The two small distal regions of WC2S matched with Bd5 whereas the interstitial and proximal regions were syntenous to Bd1. Except proximal region C-0.36 FL of WC2L, which matched with Bd1 as well as Bd5, the remaining region of WC2L had similarity with Bd5. The same region (C-0.36 FL) of WC2L also matched Bd5 for an equal number of wEST suggesting that WC2 and two brachypodium chromosomes (Bd1 and Bd5) might be originated from a common ancestral chromosome and still preserve a complex relationship. The syntenic relationship between WC2 and these two brachypodium chromosomes may be summarized as follows: WC2S-C-WC2L = Bd5/Bd1-C-Bd1/Bd5 (Figure 2). The wEST BE442655 located in pericentro-meric region of WC2S gave a hit at 51.8 Mb of Bd1 (Qi et al., 2010) suggesting the probable position of Bd1 centromere (Supplementary Table 1).

2.2.3 Wheat consensus chromosome 3 (WC3):

Out of 212 wESTs belonging to WC3, 80.7% were syntenous with Bd2 and the remaining 19.3% wESTs were syntenous with other four brachypodium chromosomes (Bd3, Bd1, Bd4 and Bd5) (Table 1). Excellent synteny conservation of WC3 was observed all along its two arms with Bd2 except few regions of partial syntenies with other brachypodium chromosomes. The summary relationship of the WC3 with the brachypodium chromosomes may be depicted as follows: WC3S-C-WC3L = Bd2-C-Bd2 (Figure 2). The wEST BE404580 mapped near the centromere of WC3L and showed synteny with long arm at 41.7 Mb of Bd2 (Qi et al. 2010). High level of synteny between WC3 and Bd2 suggest that both WC3 and Bd2 perhaps originated from a common specific ancestral chromosome.

2.2.4 Wheat consensus chromosome 4 (WC4):

From a total of 170 wESTs belonging to WC4, 82.4% were syntenic to Bd1, the remaining 17.6% being syntenic to the remaining four brachypodium chromosomes (Bd4, Bd2, Bd3 and Bd5). Therefore, WC4 is highly syntenous with a single brachypodium chromosome (Bd1) (Table 1). The order of synteny along the chromosome length was as follows: WC4S-C-WC34L = Bd1-C-Bd1 (Figure 2). The two wESTs, namely BE497309 and BF202969 spanning the pericentromeric region of WC4S and WC4L, detected syntenic positions at 59.8 Mb and 60.7 Mb, respectively in the chromosome Bd1, suggesting the possible position of Bd1 centromere (Qi et al., 2010).

2.2.5 Wheat consensus chromosome 5 (WC5):

Of the 255 wESTs belonging to WC5, 56.1% were syntenic with Bd4 and 29.4% were syntenic with Bd1 chromosome. Remaining 14.5% wESTs matched the other three brachypodium chromosomes (Bd3, Bd2 and Bd5). Complete short arm of WC5 (WC5S) matched Bd4 except the most terminal 2% region (FL 0.98-1.00) that matched with Bd3. Approximately 76% of the long arm of WC5 (WC5L) also matched with Bd4 while remaining  11% (FL 0.76-0.78, 0.78-0.79 and 0.79-0.87) and 3% (FL 0.87-1.00)  matched with Bd1 and Bd3, respectively. Interestingly, terminal regions of both the arms of WC5 matched a segment of Bd3 with only one wEST (Table 1). The syntenic pattern between WC5 and the brachypodium chromosomes may be represented as follows: WC5S-C-WC5L = Bd3/Bd4-C-Bd4/Bd1/Bd3 (Figure 2). The wheat EST BG314119 that mapped in the pericentromeric region of WC5S may indicate the location of inactive centromere of Bd4 (Qi et al., 2010).

2.2.6 Wheat consensus chromosome 6 (WC6):

Out of 194 wESTs belonging to WC6, a maximum of 78.8% matched Bd3 and only 21.2% matched with segments of remaining four brachypodium chromosomes (Bd1, Bd2, Bd4 and Bd5; Table 1). The relationship between WC6 and Bd3 was comparable to that between WC3 and Bd2. Syntenic conservation can be represented as follows: WC6S-C-WC6L = Bd3-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).

2.2.7 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 chromosomes. 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-C-Bd3/Bd1 (Figure 2). 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 rearrangements (genome reshuffling) during the period of divergence.

2.3 Consensus chromosome bins containing high density of ESTs showing homology with brachypodium

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 heterochromatic 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 2) was perhaps conserved over time, and therefore, are of evolutionary significance (Randhawa et al., 2004).

2.4 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. 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. The above 82 syntenic blocks of wheat and brachypodium 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, 0.49-0.50 (1% of the arm) and WC5L, 0.55-0.57 (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 2).

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 rearrangements 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.

2.5 Divergence between wheat-brachypodium homologs

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 . 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 3), suggesting that these evolved under purifying selection that did not alter the encoded amino acid sequence during speciation period of 35-40 million years (Huo et al., 2009; International Brachypodium Initiative, 2010). We also identified 55 fast evolving sequences with Ka/Ks ratio >1 (Figure 3). 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 (Charlesworth et al., 2001) and might be responsible for speciation in the Triticeae lineage.

2.6 Comparison of wheat and brachypodium genomes 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 50-70 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 seems that the intermediate ancestral grass genomes with n=12 had undergone chromosome reduction (also known as dysploidy) giving n=10 in sorghum (Luo et al., 2009) and maize (Salse et al., 2008); n=9 in finger millet (Srinivasachary et al., 2007); n=7 in Triticeae (Luo et al., 2009; Hackauf et al., 2009) and n=5 in brachypodium (Qi et al., 2010; International Brachypodium Initiative, 2010).

In addition to the reduction in chromosome numbers, perhaps structural differences also occur between wheat and brachypodium genomes. Consequently, with a view to decipher the structural similarities and differences between the chromosomes of wheat and brachypodium, we examined the findings of present study in relation to the 12 chromosomes of the intermediate ancestral genome reported earlier (Salse et al., 2008; International Brachypodium Initiative, 2010). In this connection, it may be noted that the 12 chromosomes of the intermediate ancestral genome underwent breakage, translocation and fusion events and reassembled into seven chromosomes of wheat and five chromosomes of brachypodium (Figure 4). As a result, two of the wheat consensus chromosomes, namely WC3 and WC6 were directly evolved from the intermediate ancestral chromosomes A1 and A2, while the remaining five wheat consensus chromosomes (WC1, WC4, WC5, WC2 and WC7) were derived following fusion of two ancestral chromosomes each. Reduction (in the course of dysploidy) in chromosome numbers i.e. n=7 in wheat, centromeres of four chromosomes of the intermediate ancestral genome (A5, A3, A4 and A6) were lost and the centromeres of intermediate ancestral chromosomes A9 and A12 perhaps combined into giving rise the centromere of wheat consensus chromosome WC5 (Qi et al., 2010; International Brachypodium Initiative, 2010).

Similarly in brachypodium, only one brachypodium chromosome (Bd5) evolved directly from the intermediate ancestral chromosome A4. The remaining four brachypodium chromosomes evolved from two or three intermediate ancestral chromosomes. For example, three brachypodium chromosomes (Bd1, Bd4 and Bd3) evolved from three intermediate ancestral chromosomes each and the remaining one chromosome Bd2 was derived from two ancestral chromosomes (Figure 4). During the above process of dysploidy leading to the evolution of five brachypodium chromosomes from the 12 chromosomes of intermediate ancestral genome, the centromeres of five chromosomes (A1, A4, A6, A8 and A12) were retained and the centromeres of the remaining seven chromosomes (A5, A7, A10, A3, A11, A2 and A9) were lost in brachypodium (Qi et al., 2010; International Brachypodium Initiative, 2010).

2.7 Wheat ESTs uniquely mapped to specific bins in wheat and their use for inferring relation with brachypodium genome

It may be recalled that as many as 793 (16.51%) wESTs (out of 4,804 bin-mapped wESTs) were mapped each to single bins; perhaps these ESTs represent each a single copy gene. These wESTs were not used for the construction of wheat consensus chromosome maps during the present study, although these may be utilized for deriving syntenic relationship between wheat and brachypodium in a manner similar to their use in determining wheat-rice synteny (Sorrells et al., 2003; La Rota and Sorrells, 2004; Singh et al., 2007). During the present study each of the single copy wESTs matched with a unique sequence of the brachypodium genome. A majority of ESTs belonging to individual chromosomes of the seven homoeologous groups (HGs) of wheat matched with sequences of either one or two brachypodium chromosomes (e.g. HG1 ESTs with Bd1 and Bd2; HG2 ESTs with Bd1 and Bd5; HG3 ESTs with Bd2; HG4 ESTs with Bd1; HG5 ESTs with Bd1 and Bd4; HG6 ESTs with Bd3 and HG7 ESTs with Bd1 and Bd3). These results of syntenic relationship between wheat and brachypodium chromosomes inferred using single copy ESTs are in agreement with the syntenic relationship determined using multi-locus wESTs.

2.8 Comparison of wheat-brachypodium synteny with previously reported wheat-rice synteny

It may be noted that wheat EST data set used for analyzing the syntenic and structural relationship between wheat and brachypodium during the present study was also used in similar earlier studies involving wheat and rice (Sorrells et al., 2003; La Rota and Sorrells, 2004). Therefore, the three-way comparison involving wheat, brachypodium and rice may help to identify the patterns of synteny relationship among the three species. A summary of this comparison is given in Table 2. We noted that WC3, WC4 and WC6 had comprehensive synteny with brachypodium chromosomes Bd2, Bd1 and Bd3, and with individual rice chromosomes R1, R3 and R2, respectively. Thus, WC3 matched with Bd2/R1, WC4 matched with Bd1/R3 and similarly WC6 matched with Bd3/R2. Therefore, it appears that the above three chromosomes of wheat, brachypodium and rice may have originated form common individual specific ancestral chromosomes as proposed in some earlier studies (Salse et al., 2008; Luo et al., 2009; Qi et al., 2010; International Brachypodium Initiative, 2010).

Further, each of the remaining four wheat consensus chromosomes (WC1, WC2, WC5 and WC7) in general showed syntenic relationship with two to three specific brachypodium chromosomes and also with two to three specific rice chromosomes (Table 2). Therefore, during the course of speciation, new chromosomes might have evolved through fusion mechanism involving at least two chromosomes. While conducting comparative genomic study involving Ae. tauschii, rice and sorghum, Luo et al. (2009) proposed that the chromosomes 2D and 7D of Ae. tauschii evolved by chromosome fusion events. A detailed comparison of the wheat-brachypodium structural synteny reported during the present study and the previously reported wheat-rice synteny may help in exploring a detailed history of genome evolution in grass lineage.

3 Conclusions

Mapped wESTs may be successfully used to examine the synteny conservation and colinearity among wheat, brachypodium and rice. Besides chromosomal rearrangements via chromosome fusion that were responsible for alteration in chromosome number, extensive synteny throughout the entire length of three wheat and brachypodium chromosomes was also discovered. It was further demonstrated that wheat brachypodium and rice largely share common syntenic pattern at chromosomal level. We also suggest that the syntenic conservation before and after polyploidization in wheat, was still maintained for at least some wheat chromosomes vis-à-vis the brachypodium and rice chromosomes. Thus, the present study shed light on the nature of chromosome evolution in polyploid genomes such as wheat and other members of Triticeae.

Author’s contributions

SK participated in the design of the study, performed analysis and drafted the manuscript. HSB and PKG participated in the design and supervision of the study and preparation of the final manuscript. All authors have read and approved the final manuscript.

Acknowledgements

The authors are thankful to the Department of Science and Technology, New Delhi, India, for the financial support to carry out this study. Thanks are also due to Professor B. Ramesh, Head, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut for providing necessary facilities. PKG held a position of NASI Senior Scientist during the tenure of which this study was completed.

References

Akhunov E.D., Goodyear A.W., Geng S., Qi L.L., Echalier B., Gill B.S., Miftahudin, Gustafson J.P., Lazo G.R., Chao S., Anderson O.D., Linkiewicz A.M., Dubcovsky J., La Rota M., Sorrells M.E., Zhang D., Nguyen H.T., Kalavacharla V., Hossain K., Kianian S.F., Peng J., Lapitan N.L.V., Gonzalez-Hernande J.L., Anderson J.A., Choi D.W., Close T.J., Dilbirligi M., Gill K.S., Walker-Simmons M.K., Steber C., McGuire P.E., Qualset C.O., and Dvorak J., 2003, The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms, Genome Res., 13: 753–763

https://doi.org/10.1101/gr.808603
PMid:12695326 PMCid:PMC430889

Bennetzen J.L., 2000, Sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions, Plant Cell, 12: 1021–1030

https://doi.org/10.2307/3871252
PMid:10899971 PMCid:PMC149046

Bolot S., Abrouk M., Masood-Quraishi U., Stein N., Messing J., Feuillet C., and Salse J., 2009, The ‘inner circle’ of the cereal genomes, Curr. Opin. Plant Biol., 12: 119–125

https://doi.org/10.1016/j.pbi.2008.10.011
PMid:19095493

Bortiri E., Coleman–Derr D., Lazo G.R., Anderson O.D., and Gu Y.Q., 2008, The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes, BMC Res. Notes, 1: 61

https://doi.org/10.1186/1756-0500-1-61
PMid:18710514 PMCid:PMC2527572

Bossolini E., Wicker T., Knobel P.A., Keller B., 2007, Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation, Plant J., 49: 704–717

https://doi.org/10.1111/j.1365-313X.2006.02991.x
PMid:17270010

Chantret N., Cenci A., Sabot F., Anderson O., and Dubcovsky J., 2004, Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice, Mol. Genet. Genomics, 271: 377–386

https://doi.org/10.1007/s00438-004-0991-y
PMid:15014981

Conley E.J., Nduati V., Gonzalez–Hernandez J.L., Mesfin A., Trudeau-Spanjers M., Chao S., Lazo G.R., Hummel D.D., Anderson O.D., Qi L.L., Gill B.S., Echalier B., Linkiewicz A.M., Dubscovsky J., Akhunov E.D., Dvorak J., Peng J.H., Lapitan N.L.V., Pathan M.S., Nguyen H.T., Ma X-F., Miftahudin, Gustafson J.P., Greene R.A., Sorrells M.E., Hossain K.G., Kalavacharla V., Kianian S.F., Sidhu D., Dilbirligi M., Gill K.S., Choi D.W., Fenton R.D., Close T.J., McGuire P.E., Qualset C.O., and Anderson J.A., 2004, A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice, Genetics, 168: 625-637

https://doi.org/10.1534/genetics.104.034801
PMid:15514040 PMCid:PMC1448822

Devos K.M., 2010, Grass genome organization and evolution, Curr. Opin. Plant Biol., 13: 139–145

https://doi.org/10.1016/j.pbi.2009.12.005
PMid:20064738

Distelfeld A., Uauy C., Olmos S., Schlatter A.R., Dubcovsky J., and Fahima T., 2004, Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2, Funct. Integr. Genomics, 4: 59–66

https://doi.org/10.1007/s10142-003-0097-3
PMid:14752608

Draper J., Mur L.A.J., Jenkins G. Ghosh-Biswas G.C., Bablak P., Hasterok R., and Routledge A.P.M., 2001, Brachypodium distachyon. A new model system for functional genomics in grasses, Plant Physiol., 127: 1539–1555

https://doi.org/10.1104/pp.010196
PMid:11743099 PMCid:PMC133562

Freeling M., 2001, Grasses as a single genetic system. Reassessment 2001. Plant Physiol., 125: 1191–1197

https://doi.org/10.1104/pp.125.3.1191
PMid:11244100 PMCid:PMC1539374

Gill B.S., Friebe B., and Endo T.R., 1991, Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum), Genome, 34: 830–839

https://doi.org/10.1104/pp.125.3.1191
PMid:11244100 PMCid:PMC1539374

Gill K.S., Gill B.S., Endo T.R., and Boyko E.V., 1996a, Identification and high–density mapping of gene–rich regions in chromosome group 5 of wheat, Genetics, 143: 1001–1012

https://doi.org/10.1104/pp.125.3.1191
PMid:11244100 PMCid:PMC1539374

Gill K.S., Gill B.S., Endo T.R., and Taylor T., 1996b, Identification and high–density mapping of gene–rich regions in chromosome group 1 of wheat. Genetics, 144: 1883–1891

https://doi.org/10.1093/genetics/144.4.1883
PMid:8978071 PMCid:PMC1207735

Gu Y.Q., Ma Y., Huo N., Vogel J.P., You F.M., Lazo G.R., Nelson W.M., Soderlund C., Dvorak J., Anderson O.D., and Luo M.C., 2009, A BAC–based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat, BMC Genomics, 10: 496

https://doi.org/10.1186/1471-2164-10-496
PMid:19860896 PMCid:PMC2774330

Hackauf B., Rudd S., Voort J.R.V, Miedaner T., and Wehling P., 2009, Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome, Theor. Appl. Genet., 118: 371–384

https://doi.org/10.1007/s00122-008-0906-0
PMid:18953524

Hossain K.G., Kalavacharla V., Lazo G.R., Hegstad J., Wentz M.J., Kianian P.M.A., Simons K., Gehlhar S., Rust K.L., Syamala R.R., Obeori K., Bhamidimarri S., Karunadharma P., Chao S., Anderson D.,  Qi L.L., Echalier B., Gill B.S., Linkiewicz A.M., Ratnasiri A., Dubcovsky J., Akhunov E.D., Dvorak J., Miftahudin, Ross K., Gustafson J.P., Radhawa H.S., Dilbirligi M., Gill K.S., Peng J.H., Lapitan N.L.V., Greene R.A., Bermudez-Kandianis C.E., Sorrells M.E., Feril O., Pathan M.S., Nguyen H.T., Gonzalez-Hernandez J.L., Conley E.J., Anderson J.A., Choi D.W., Fenton, Close T.J., McGuire P.E., Qualset C.O., and Kianian S.F., 2004, A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7, Genetics, 168: 687–699

https://doi.org/10.1534/genetics.104.034850
PMid:15514045 PMCid:PMC1448827

Huo N., Gu Y.Q., Lazo G.R., Vogel J.P., Coleman-Derr D., Luo M.C., Thilmony R., Garvin D.F., and Anderson O.D., 2006, Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics, Genome, 49: 1099–1108

https://doi.org/10.1534/genetics.104.034850
PMid:15514045 PMCid:PMC1448827

Huo N., Lazo G.R., Vogel J.P., You F.M., Ma Y., Hayden D.M., Coleman-Derr D., Hill T.A., Dvorak J., Anderson O.D., Luo M.C., and Gu Y.Q., 2008, The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences, Funct. Integr. Genomics, 8: 135–147

https://doi.org/10.1534/genetics.104.034850
PMid:15514045 PMCid:PMC1448827

Huo N., Vogel J.P., Lazo G.R., You F.M., Ma Y., McMohan S., Dvorak J., Anderson O.D., Luo M.C., and Gu Y.Q., 2009, Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat, Plant Mol. Biol., 70: 47–61

https://doi.org/10.1007/s11103-009-9456-3
PMid:19184460

International Brachypodium Initiative, 2010, Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature, 463: 763–768

https://doi.org/10.1038/nature08747
PMid:20148030

International Rice Genome Sequencing Project, 2005, The map–based sequence of the rice genome, Nature, 436: 793–800

https://doi.org/10.1038/nature03895
PMid:16100779

Kellogg E.A., 2001, Evolutionary history of the grasses, Plant Physiol. 125: 1198-1205

https://doi.org/10.1104/pp.125.3.1198
PMid:11244101 PMCid:PMC1539375

Kumar S., Mohan A., Balyan H.S., and Gupta P.K., 2009, Orthology between genomes of Brachypodium, wheat and rice, BMC Res. Notes, 2: 93

https://doi.org/10.1186/1756-0500-2-93
PMid:19470185 PMCid:PMC2695472

La Rota M., and Sorrells M.E., 2004, Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat, Funct. Integr. Genomics, 4: 34–46

https://doi.org/10.1007/s10142-003-0098-2
PMid:14740255

Larkin D.M., Pape G., and Donthu R., 2009, Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories, Genome Res., 19: 770–777

https://doi.org/10.1101/gr.086546.108
PMid:19342477 PMCid:PMC2675965

Li W., and Gill B.S., 2002, The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the Triticeae, Genetics, 160: 1153–1162

https://doi.org/10.1093/genetics/160.3.1153
PMid:11901130 PMCid:PMC1462018

Librado P., and Rozas J., 2009, DnaSP v5: A software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25: 1451–1452

https://doi.org/10.1093/bioinformatics/btp187
PMid:19346325

Linkiewicz A.M., Qi L.L., Gill B.S., Ratnasiri A., Echalier B., Chao S., Lazo G.R., Hummel D.D., Anderson O.D., Akhunov E.D., Dvorak J., Pathan M.S., Nguyen H.T., Peng J.H., Lapitan N.L.V., Miftahudin, Gustafson J.P., La Rota C.M., Sorrells M.E., Hossain K.G., Kalavacharla V., Kianian S.F., Sandhu D., Bondaeva S.N., Gill K.S., Conley E.J., Anderson J.A., Fenton R.D., Close T.J., McGuire P.E., Qualset C.O., and Dubcovsky J., 2004, A 2500–locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice, Genetics, 168: 665–676

https://doi.org/10.1534/genetics.104.034835
PMid:15514043 PMCid:PMC1448825

Luo M.C., Deal K.R., Akhunov E.D., Akhunova A.R., Anderson O.D., Anderson J.A., Blake N., Clegg M.T., Coleman-Derr D., Conley E.J., Crossman C.C., Dubcovsky J., Gill B.S., Gu Y.Q., Hadam J., Heo H.Y., Huo N., Lazo G., Ma Y., Mathews D.E., McGuire P.E., Morrel P.L., Qualset C.O., Renfro J., Tabanao D., Talbert L.E., Tian C., Toleno D.M., Warburton M.L., You F.M., Zhang W., and Dvorak J., 2009, Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae, Proc. Natl. Acad. Sci. USA., 106: 15780–15785

https://doi.org/10.1073/pnas.0908195106
PMid:19717446 PMCid:PMC2747195

Mayers K.F.X., Martis M., Hedley P.E., Simkova H., Liu H., Mirris J.A., Steuernagel B., Taudien S., Roessner S., Gundlach H., Kubalakova M., Schankova P., Murat F., Felder M., Nussbaumer T., Graner A., Salse J., Endo T., Sakai H., Tanaka T., Itoh T., Sato K., Platzer M., Matsumoto T., Scholz U., Dolezel J., Waugh R., and Stein N., 2011, Unlocking the barley genome by chromosomal and comparative genomics, Plant Cell, 23: 1249-1263

https://doi.org/10.1105/tpc.110.082537
PMid:21467582 PMCid:PMC3101540

Moore G., Devos K.M., Wang Z., and Gale M.D, 1995b, Grasses, line up and form a circle, Curr. Biol., 5: 737–739

https://doi.org/10.1105/tpc.110.082537
PMid:21467582 PMCid:PMC3101540

Moore G., Foote T., Helentjaris T., Devos K., Kurata N., and Gale M.D., 1995a, Was there a single ancestral cereal chromosome? Trends Genet., 11: 81–82

https://doi.org/10.1016/S0168-9525(00)89005-8

Munkvold J.D., Greene R.A., Bermudez–Kandianis C.E., La Rota M., Edwards H., Sorrells S.F., Dake T., Benscher D., Kantety R., Linkiewicz A.M., Dubcovsky J., Miftahudin, Gustafson J.P., Pathan M.S., Nguyen H.T., Matthews D.E., Chao S., Lazo G.R., Hummel D.D., Anderson O.D., Anderson J.A., Gonzalez-Hernandez J.L., Peng J.H., Lapitan N., Qi L.L., Echalier B., Gill B.S., Hossain K.G., Kalavacharla V., Kianian S.F., Sandhu D., Erayman M., Gill K.S., McGuire P.E., Qualset C.O., and Sorrells M.E., 2004, Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1, Genetics, 168: 639–650

https://doi.org/10.1016/S0168-9525(00)89005-8

Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J., Spannag M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J., Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M., Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L., Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P., Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman, Ware D., Westhoff P., Mayer K.F.X., Messing J., and Rokhsar D.S., 2009, The Sorghum bicolor genome and the diversifcation of grasses, Nature, 457: 551–556

https://doi.org/10.1038/nature07723
PMid:19189423

Qi L.L., Echalier B., Chao S., Lazo G.R., Butler G.E., Anderson O.D., Akhunov E.D., Dvorak J., Linkiewicz A.M., Ratnasiri A., Dubcovsky J., Bermudez-Kandianis C.E., Greene R.A., Kantety R., La Rota C.M., Munkvold J.D., Sorrells S.F., Dilbirligi M., Sidhu D., Erayman M., Randhawa H.S., Sandhu D., Bondareva S.N., Gill K.S., Mahmoud A.A., MA X-F.,  Miftahudin,  Gustafson J.P., Conley A.J., Nduati V., Gonzalez-Hernandez J.L., Anderson J.A., Peng J.H., Lapitan N.L.V., Hossain K.G., Kalavacharla V., Kianian S.F., Pathan M.S., Zhang D.S., Nguyen H.T., Choi D.W., Fenton R.D., Close T.J., McGuire P.E., Qualset C.O., and Gill B.S., 2004, A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploidy wheat, Genetics, 168: 701–712

https://doi.org/10.1534/genetics.104.034868
PMid:15514046 PMCid:PMC1448828

Qi L., Friebe B., Wu J., Gu Y., Qian C., and Gill B.S., 2010, The compact Brachypodium genome conserve centromeric regions of a common ancestor with wheat and rice, Funct. Integr. Genomics, 10: 477–492

https://doi.org/10.1007/s10142-010-0190-3
PMid:20842403

Randhawa H.S., Dilbirligi M., Sidhu D., Erayman M., Sandhu D., Bondareva S., Chao S., Lazo G.R., Anderson O.D., Miftahudin, Gustafson J.P., Echalier B., Qi L.L., Gill B.S., Akhunov E.D., Dvorak J., Linkiewicz A.M., Ratnasiri A., Dubcovsky J., Bermudez-Kandianis C.E., Greene R.A., Sorrells S.F., Conley E.J., Anderson J.A., Peng J.H., Lapitan N.L.V., Hossain K.G., Kalavacharla V., Kianian S.F., Pathan M.S., Nguyen H.T., Endo T.R., Close T.J., McGuire P.E., Qualset C.O., and Gill K.S., 2004, Deletion mapping of homoeologous group 6–specific wheat expressed sequence tags, Genetics, 168: 677–686

https://doi.org/10.1534/genetics.104.034843
PMid:15514044 PMCid:PMC1448826

Rubin G.M., Yandell M.D., and Wortman J.R., 2000, Comparative genomics of the eukaryotes, Science, 287: 2204–2215

https://doi.org/10.1534/genetics.104.034843
PMid:15514044 PMCid:PMC1448826

Salse J., Bolot S., Throude M., Jouffe V., Piegu B., Quraishi U.M., Calcagno T., Cooke R., Delseny M., and Feuillet C., 2008, Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution, Plant Cell, 20: 11–24

https://doi.org/10.1105/tpc.107.056309
PMid:18178768 PMCid:PMC2254919

Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D., Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K., Fronick C., Courtney B., Rock S.M., Belter E., Du F., Kim K., Abbott R.M., Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M., Gillam B., Chen W., Yan L., Higginbotham J., Cardenas M., Waligorski J., Applebaum E., Phelps L., Falcone J., Kanchi K., Thane T., Scimone A., Thane N., Henke J., Wang T., Ruppert J., Shah N., Rotter K., Hodges J., Ingenthron E., Cordes M., Kohlberg S., Sgro J., Delgado B., Mead K., Chinwalla A., Leonard S., Crouse K., Collura K., Kudrna D., Currie J., He R., Angelova A., Rajasekar S., Mueller T., Lomeli R., Scara G., Ko A., Delaney K., Wissotski M., Lopez G., Campos D., Braidotti M., Ashley E., Golser W., Kim H.R., Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A., Fan C., Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T., Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L., Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Buren P.V., Vaughn M.W., Ying K., Yeh C-T., Emrich S.J., Jia Y., Kalyanaraman A., Hsia A-P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C., Chaparro C., Chia J-M., Deragon L-M., Estill J.C., Fu Y., Jeddeloh J.A., Han J., Lee H., Li P., Lisch D.R., Liu S., Liu Z., Nagel D.H., McCann M.C., Miguel P.S., Myers A.M., Nettleton D., Nguyen J., Penning B.W., Ponnala L., Schneider K.L., Schwartz D.C., Sharma A., Soderlund C., Springer N.M., Sun Q., Wang H., Waterman M., Westerman R., Wolfgruber T.K., Yang L., Yu U., Zhang L., Zhou S., Zhu Q., Bennetzen, Dawe R.K., Jiang J., Jiang N., Presting G.G., Wessler S.R., Aluru S., Martienssen R.A., Clifton S.W., McCombie W.R., Wing R.A., and Wilson R.K., 2009, The B73 maize genome: complexity, diversity and dynamics, Science, 326: 1112–1115

https://doi.org/10.1105/tpc.107.056309
PMid:18178768 PMCid:PMC2254919

Schnurbusch T. Collins N.C., Eastwood R.F., Sutton T., Jefferies S.P., and Langridge P., 2007, Fine mapping and targeted SNP survey using rice–wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat, Theor. Appl. Genet., 115: 451–461

https://doi.org/10.1007/s00122-007-0579-0
PMid:17571251

Singh N.K., Dalal V., Batra K., Singh B.K., Chitra G., Singh A., Ghazi I.A., Yadav M., Pandit A., Dixit R., Singh P.K., Singh H., Koundal K.R., Gaikwad K., Mohapatra T., and Sharma T.R., 2007, Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes, Funct. Integr. Genomics, 7: 17–35

https://doi.org/10.1007/s10142-006-0033-4
PMid:16865332

Sorrells M.E., La Rota M., Bermudez-Kandianis C.E., Greene R.A., Kantety R., Munkvold J.D., Miftahudin, Mahmoud A., Ma X., Gustafson P.J., Qi L.L., Echalier B., Gill B.S., Matthews D.E., Lazo G.R., Chao S., Anderson O.D., Edwards H., Linkiewicz A.M., Dubcovsky J., Akhunov E.D., Dvorak J., Zhang D., Nguyen H.T., Peng J., Lapitan N.L.V., Gonzalez-Hernandez J.L., Anderson J.A., Hossain K., Kalavacharla V., Kianian S.F., Choi D-W., Close T.J., Dilbirligi M., Gill K.S., Steber C., Walker-Simmons M.K., McGuire P.E., and Qualset C.O., 2003, Comparative DNA sequence analysis of wheat and rice genomes, Genome Res, 13: 1818–1827

https://doi.org/10.1101/gr.1113003
PMid:12902377 PMCid:PMC403773

Srinivasachary, Dida M.M., Gale M.D., and Devos K.M., 2007, Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes, Theor. Appl. Genet., 115: 489–499

https://doi.org/10.1007/s00122-007-0582-5
PMid:17619853

Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S., 2011, MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., doi: 10.1093/molbev/msr121

https://doi.org/10.1093/molbev/msr121
PMid:21546353 PMCid:PMC3203626

Thiel T., Graner A., Waugh R., Grosse I., Close T.J., and Stein N., 2009, Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice, BMC Evol. Biol., 9: 209–226

https://doi.org/10.1186/1471-2148-9-209
PMid:19698139 PMCid:PMC2746218

Vogel J.P., Garvin D.F., Leong O.M., and Hayden D.M., 2006, Agrobacterium–mediated transformation and inbred line development in the model grass Brachypodium distachyon, Plant Cell Tissue Organ Cult., 85: 199–211

https://doi.org/10.1007/s11240-005-9023-9

Wei F., Coe E., Nelson W., Bharti A.K., Engler F., Butler E., Kim H., Goicoechea J.L., Chen M., Lee S., Fuks G., Sanchez-Villeda H., Schroeder S., Fang Z., McMullen M., Davis G., Bowers J.E., Paterson A.H., Schaeffer M., Gardiner J., Cone K., Messing J., Soderlund C., and Wing RA., 2007, Physical and genetic structure of the maize genome reflects its complex evolutionary history, PLoS Genet., 3: e123

https://doi.org/10.1007/s11240-005-9023-9

Wicker T., Buchmann J.P., and Keller B., 2010, Patching gaps in plant genomes results in gene movement and erosion of colinearity, Genome Res., 20: 1229–1237

https://doi.org/10.1101/gr.107284.110
PMid:20530251 PMCid:PMC2928501