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First published online October 1, 2004; 10.1104/pp.104.044081 Plant Physiology 136:3177-3190 (2004) © 2004 American Society of Plant Biologists Comparative Sequence Analysis of the Region Harboring the Hardness Locus in Barley and Its Colinear Region in Rice1Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (K.S.C., W.P.); and School of Agriculture and Wine (K.S.C., P.L.) and Australian Centre for Plant Functional Genomics (P.L.), University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
The ancestral shared synteny concept has been advocated as an approach to positionally clone genes from complex genomes. However, the unified grass genome model and the study of grasses as a single syntenic genome is a topic of considerable controversy. Hence, more quantitative studies of cereal colinearity at the sequence level are required. This study compared a contiguous 300-kb sequence of the barley (Hordeum vulgare) genome with the colinear region in rice (Oryza sativa). The barley sequence harbors genes involved in endosperm texture, which may be the subject of distinctive evolutionary forces and is located at the extreme telomeric end of the short arm of chromosome 5H. Comparative sequence analysis revealed the presence of five orthologous genes and a complex, postspeciation evolutionary history involving small chromosomal rearrangements, a translocation, numerous gene duplications, and extensive transposon insertion. Discrepancies in gene content and microcolinearity indicate that caution should be exercised in the use of rice as a surrogate for map-based cloning of genes from large genome cereals such as barley.
Gene content among higher eukaryotes appears to be relatively constant, ranging from 25,000 to 43,000 genes even though the genome size varies by 600-fold among angiosperms alone (Bennett et al., 1982  ; Bennett and Leitch, 1995, 1997; Miklos and Rubin, 1996). In the Gramineae, the allohexaploid genome of bread wheat (Triticum aestivum; 17,000 Mb) is approximately 3, 6, and 35 times larger than the barley (Hordeum vulgare; 5,300 Mb), maize (Zea mays; 2,500 Mb), and rice (Oryza sativa; 440 Mb) genomes, respectively (Arumuganathan and Earle, 1991; Shields, 1993). Comparative mapping studies have shown that, despite substantial variation in genome size and chromosome number, grass species have maintained significant conservation of gene and marker order (colinearity) and have sustained a minimal number of large chromosomal rearrangements since their divergence 50 to 80 million years ago (Wolfe et al., 1989; Crepet and Feldman, 1991; Ahn and Tanksley, 1993; Clark et al., 1995; Moore et al., 1995; Devos and Gale, 1997; Gale and Devos, 1998; Keller and Feuillet, 2000). The high degree of observed colinearity, coupled with the assumption that the essential components for growth and development are conserved among plants, led to the use of model organisms with small genome sizes, namely Arabidopsis and rice, as tools for plant genomics studies.
Despite the apparent conservation of gene order and content on a full genome scale, at the local level various small chromosomal rearrangements, such as segmental inversions, translocations, insertions, and deletions, have been reported to disrupt the degree of microcolinearity (for review, see Bennetzen, 2000
Although several studies have described the levels of microcolinearity between Triticeae species and rice (Kilian et al., 1997
This paper describes the generation and sequencing of a contiguous genomic region of the barley genome represented by three bacterial artificial chromosomes (BACs) that cover the Ha locus and comparison with the colinear genomic region in rice. Our results indicate that comparative genomics can be an invaluable resource for the identification and determination of gene structure and provide new insights in the processes of genome evolution. However, the extensive number of small chromosomal rearrangements, including the absence of the entire grain (endosperm) texture gene family in rice, could complicate shuttle mapping and cloning approaches (Delseny, 2004
Identification and Sequencing of Barley BAC Clones
Fluorescent-based fingerprinting of 14 BACs believed to harbor the grain softness protein (GSP) gene identified BAC122.a5 as the clone that exhibited the most extensive coverage of the genomic region flanking the GSP locus. To extend this physical region to include the genetically linked hordoindoline genes (Rouves et al., 1996
Gene Density of the Barley Genomic Region The gene density of this region was determined through the integration of several different gene prediction applications and homology to previously characterized genes and expressed sequence tags (ESTs) available in the public databases. In total, 12 putative protein-coding and two duplicated tRNAARG genes (Fig. 1A) were identified within the 303-kb contiguous sequence. All exon:intron splice junctions contained the conserved GT and AG intron borders and a minimum of five of the nine (5'-CAG:GTAAGT-3') and three of the five (5'-GCAG:G-3') consensus nucleotides for the respective exon:intron and intron:exon splice sites in plants, with one exception. The border between exon 1 and intron 1 of the putative synaptobrevin (vesicle associated membrane protein, HvVAMP) gene contained only four of the nine exon:intron consensus nucleotides. However, both the presence of the mandatory GT intron border and splice agreement with more than one EST provided further support that this is a functional splice site. Three of the four candidate grain texture genes, hinb-1, hinb-2, and hina, were found in the same orientation. However, HvGSP was in the opposite orientation (Fig. 1A). Homology at the protein level suggests that all four are members of the same gene family and may have resulted from duplications of a single ancestral gene. Based on nucleotide sequence homology, the original duplication resulted in HvGSP and one of the hordoindoline genes. Subsequent duplications generated templates for the gradual divergence of hina and hinb and an additional hinb copy.
Three of the putative genes belong to the ATPase associated activities superfamily characterized by one or two conserved domains (ATPase associated activities modules) responsible for ATP binding (Patel and Latterich, 1998
Three out of the five remaining genes showed significant homology to previously described proteins: naringenin-chalcone synthase (HvCHS), N-acetylglucosaminyltransferase (HvGlcNAc), and synaptobrevin (HvVAMP), a vesicle associated membrane protein. CHS is a member of the chalcone synthase gene family. Chalcone is a key compound in the phenylpropenoid pathways involved in various cellular functions, including flower pigmentation (anthocyanin) and microbial defense (phytoalexins; Dixon et al., 1995 , 1996; Dixon and Paiva, 1995; Shirley, 1996). Synaptobrevin is involved in a complex of SNARE proteins that control the regulation of vesicle docking and fusion during transport (Trimble et al., 1988; Baurnert et al., 1989; Sollner et al., 1993; Weber et al., 1998; Chen and Scheller, 2001). GlcNAc is a member of the large enzymatic superfamily of UDP glycosyltransferases. UDP glycosyltransferases regulate the transfer of sugar molecules (glycosyl residues) between different chemical R-groups (aglycones), thus indirectly regulating the biochemical properties of aglycones, i.e. secondary metabolites involved in abiotic stress and defense responses, hormones, and foreign chemical substances (xenobiotics, such as pesticides and herbicides; Li et al., 2001; Ross et al., 2001). Two additional putative genes (HvPG1 and HvPG2) whose functions remain to be determined are also present in the contig. Although EST homology is low (pLog > E-6) for both genes and is limited to members of the grass family, HvPG2 shows significant protein homology (pLog  E-44) to several predicted proteins from mammalian species, including Rattus norvegicus, Homo sapiens, and Mus musculus (GI accession nos. 34867764, 13376072, and 21313472, respectively).
Over 75% of the contiguous barley sequence was composed of repetitive elements (Table I). The position, orientation, and order of insertion of the different transposable elements are depicted in Figure 2. The major portion of insertional activity has been directed to the intergenic space between hinb-1 and hina and between HvGSP and HvPG2. Approximately 93% of the 78-kb region separating hinb-1 and hina is composed of two separate nested element clusters. The Sukkula_AY643843_1 solo long terminal repeat (LTR), the BARE-1_AY643843_1 retrotransposon, and the truncated Inga_AY643843 retrotransposon represent the last of a series of insertions forming the largest of the two clusters involving the now degenerate CACTA transposon and BAGY-2_AY643843, Sabrina_AY643843_1, and Lolaog_AY643843 retrotransposons. The smaller cluster is composed of the full-length Caspar_AY643843_2 transposon immediately flanked by two identical putative short interspersed nuclear elements (SINEs; Dido_AY643843_1 and Dido_AY643843_2). All three elements are inserted into the extreme 5' end of the novel long interspersed nuclear element (LINE) Persephone_AY643843.
The 97-kb intergenic space between HvGSP and HvPG2 is also primarily composed (97%) of two independent transposable element clusters. The insertion of the novel copia-like element Maximus_AY643844 provided a platform for eight additional independent insertions including a highly degenerate element with identifiable inverted repeats, an intact 5-bp target site duplication (TSD), and remnants of ancient coding capacity and seven retrotransposons: Sabrina_AY643844_2, BARE-1_AY643844_2, the novel Latidu-like Vagabond_AY643844, and four BARE-2 (BARE-2_AY643844_1–4; two remain only as solo LTRs). Likewise, the degenerate HORGY_AY643844 retrotransposon acted as the receptor for the insertion of the novel gypsy-like element Haight_AY643844 and an additional BARE-1 copy (BARE-1_AY643844_3).
Two other examples of nested transposable elements are found within the contiguous barley sequence. A second Sukkula solo LTR (Sukkula_AY643843_2) was found inserted into the only terminal-repeat retrotransposons in miniature (TRIM) within the region (TRIM_AY643843). This small cluster is located between the HvCHS and HvVAMP genes. Similarly, the full-length BARE-1_AY643844_4 and the BARE-1_AY643844_5 solo LTR were found sequentially inserted into the novel gypsy element Ashbury_AY643844_2. This cluster is located downstream of HvPG2. In addition, a second copy of Ashbury (Ashbury_AY643842_1) appears to have inserted into a second Caspar (Caspar_AY643842_1) transposon. However, the entire sequence of both elements could not be obtained as they extend beyond the extreme 5' end of the contig. Likewise only the partial sequence of an additional BARE-2 (BARE-2_AY643844_5) element was found as a consequence of its location at the extreme 3' end of the contig. A second novel LINE, Morpheus_AY643843, was found located just upstream of
In total, 15 different miniinverted transposable element (MITE) insertions were found composing less than 1% of the total genomic region. The majority of these were members of the Stowaway and Tourist families contributing seven and four respective copies. One full-length and one partial copy of the XI element were also located in the region. This element, previously described as a potential novel element (Brunner et al., 2003
To facilitate a comparison between rice and barley sequences, all repetitive elements were removed from the barley genomic sequence and flanking segments were merged at the site of target duplication. The resulting 69-kb barley sequence was used as a template for additional searches of the nonredundant database (nrdb) and EST database (dbEST) at the National Center of Biotechnology Information (NCBI). Several regions of considerable homology were identified across a 34-kb unannotated segment of rice chromosome 12 (GenBank accession nos. AL928743 and AL732378). All seven conserved regions corresponded to the genic space of the barley contig, and no significant sequence identity longer than 25 bp was found beyond the coding regions of the genes.
Similar to the barley region, the rice region also contains three ATPase gene copies (Fig. 1B). However, a greater degree of sequence homology exists among paralogs within species than between orthologs of the different species. This indicates that gene duplication occurred independently post speciation (Fig. 3). OsATPase-3 is the only functional rice copy encoding a 524-amino acid protein with 68% and 72% identity (82% similarity) to
A TBLASTN comparison using the GSP protein identified a small stretch of 120 bp in the colinear rice sequence with high similarity (64%; E = 0.55) to the C-terminal end of the protein. This putative unannotated rice protein was previously identified through a similar comparison using the monococcum GSP gene, and further analysis revealed the presence of both a putative TATA-box and polyadenylation signal (Chantret et al., 2004 Homologs to four of the five remaining barley genes were located within the colinear region of rice. However, the orientation and organization of these genes is not entirely conserved between the two grass species (Fig. 1). A chromosomal rearrangement has reversed the positions of two gene clusters (an ATPase and PG1 and VAMP, GlcNAc, GSP, and PG2) while maintaining gene order and orientation within clusters. Although a CHS homolog is not present within the colinear rice region, a homolog with 91% identity at the nucleotide level exists on rice chromosome 7 (GI number 34395291). This suggests a past translocation event involving either the relocation of CHS from chromosome 12 to chromosome 7 in rice or of CHS from another region of the barley genome to the region surrounding the Ha locus (Fig. 3).
The gene structure of the barley and rice orthologs was compared to Arabidopsis using BLASTP and BLASTN searches at The Arabidopsis Information Resource (TAIR; http://www.arabidopsis.org/Blast/; Table II). Grain texture homologs could not be detected through BLASTN searches. The highest protein similarities were 48% to the C-terminal end of a seed storage protein (At4g27140; score 39.5; E = 0.002) and 39% to the N-terminal end of a protease inhibitor/seed storage/lipid transfer protein (At3g42720; score 32.1; E = 0.26).
The putative barley ATPases were the only gene products within the contig to maintain a higher similarity to the Arabidopsis (At5g40010; 75% similarity; Table I) than the closest rice homolog (72%). The ATPases of all three species contained a single exon. The predicted HvPG1 protein (535 amino acids) shows 87% and 67% similarity to the predicted OsPG1 protein (526aa) and that of the closest Arabidopsis homolog (At1g74780, 533 amino acids; Table I). All three genes contain two exons. However, neither exon is of similar length in any of the three species (Fig. 4A). The gene structure in barley and rice was confirmed by alignment of the genomic sequence with Triticeae and rice ESTs, respectively (Table I). Although the precise function of this gene has yet to be determined, the Arabidopsis homolog is annotated as containing similarity to a nodule-specific protein in Lotus japonicus (GI no. 3329366).
The predicted HvCHS (432 amino acids) gene product showed a high level of similarity to its closest rice (GI no. 34395291; 405 amino acids; 87% similarity) and Arabidopsis (At4g3450; 392 amino acids; 78% similarity) homologs (Table I). The gene structure in barley was confirmed by alignment of the genomic sequence with wheat and barley ESTs (Table I). Both the rice and barley genes contain two exons and the Arabidopsis gene contains three exons (Fig. 4B). Exon 1 from all three species differs in length by only nine codons. The main difference between exon 2 from Arabidopsis and rice is the presence of a (GC)9 microsatellite just before the stop codon in rice. Interestingly, the translated amino acids of the rice microsatellite are conserved in the barley protein although the microsatellite structure is no longer present. Exon 2 of HvCHS contains an additional stretch of 23 codons not found in either of the other two species.
A good similarity exists between the HvVAMP protein (215 amino acids) and both the OsVAMP protein (219 amino acids; 90% similarity) and closest Arabidopsis homolog (At1g04760; 220 amino acids; 84% similarity; Table I). The gene structure in barley and rice was confirmed by alignment of the genomic sequence with wheat and rice ESTs (Table I). However, two rice ESTs (GenBank accession nos. CB667109 and CB667110) showed that the second intron of the rice transcript was not being spliced. Both the 5' and 3' splice sites show homology to the 5'-CAG:GTAAGT-3' and 5'-GCAG:G-3' plant consensus sites and the uracil/adenine content of the intron is within the expected range. However, intron 2 does not contain a strong branchpoint consensus and this could reduce splice efficiency (Simpson et al., 2002 The predicted HvGlcNAc and OsGlcNAc proteins are almost identical in length (425 versus 426 amino acids, respectively) and demonstrate a high degree of similarity (87%; Table I). The slightly larger Arabidopsis homolog (At5g39990; 447 amino acids) is 76% similar to both the barley and rice proteins. The gene structure in barley and rice was confirmed by alignment of the genomic sequence with barley, sorghum, and rice ESTs (Table I). Exons 2 and 3 are identical in length in all three species, and exon 4 is identical in length in Arabidopsis and rice. In addition, the first and fourth exons of HvGlcNAc differ in length from those of OsGlcNAc by only three and two codons, respectively (Fig. 4D). Alternative splicing in Arabidopsis to conserve the length of the first exon is highly unlikely as six of the nine consensus bases are absent including the mandatory GT at the site of excision.
A high level of similarity exists between the HvPG2 protein (753 amino acids) and both the OsPG2 protein (683 amino acids; 84% similarity) and the closest Arabidopsis homolog (At1g74790; 695 amino acids; 72% similarity; Table I). The gene structure in barley and rice was confirmed by alignment of the genomic sequence with wheat and rice ESTs, respectively (Table I). However, no homologous ESTs were found for the extreme 5' end of either gene. Therefore, two alternate structures for the barley protein were considered. The first, predicted by the rice genome automated annotation system (RiceGAAS; Sakata et al., 2002
Gene Islands and Intergenic Space
This study describes the sequencing and analysis of a region of the barley genome covering over 300 kb at 10 times coverage. The current gene content of higher plants is estimated to range from 25,000 to 43,000 genes (Miklos and Rubin, 1996
The presence of different transposable elements within the barley contig was the primary contributor to the patterns of genome organization and the major factor responsible for the vast difference in length between the colinear rice and barley sequences. Although over 75% of the barley contiguous region reported here is composed of repetitive elements, only one element, a 5-kb Ty1/copia retrotransposon, was present within the orthologous rice sequence (Fig. 1B). One-third of the repetitive sequence in the barley region consists of the BARE retrotransposon family, with both BARE-1 and BARE-2 contributing equally. This is 3-fold higher than average genome BARE-1 levels estimated in cultivated barley. However, other members of the Hordeae were found to have as much as 40% of their genomes composed of BARE-1 alone (Vicient et al., 1999
It is interesting that the only retrotransposon insertion in the rice sequence occurred within the
It has been suggested that differences in intron length could also account for a portion of the differences observed in genome size. A greater proportion of rice introns (64%) were longer than their barley counterparts. However, the total length of intron sequence within a given gene was equally as likely to be longer in barley as in rice (two versus three genes, respectively; Fig. 4). When the introns of rice and Arabidopsis were compared, all but one rice intron was longer, and the total intron length within a gene was always greater for the rice gene. Interestingly this was not the case when comparing the barley and Arabidopsis genes despite a considerably larger difference in genome size. Although a greater number of barley introns (69%) were longer than their Arabidopsis equivalents, only three of the five genes gained extra additive length (Fig. 4). In both cases, the longer total intron length in Arabidopsis was a result of an extra intron. Although longer intron size within the grass genes suggests either a greater frequency of large insertions or a better retention of such insertions, this may be compensated for by a greater number of smaller introns within Arabidopsis genes. Similar comparisons in intron length were reported in barley BAC 635P2 (Dubcovsky et al., 2001
Despite the extensive collection of ESTs in the public database, sequences of full-length ESTs are still fairly rare. In addition, ESTs for a particular gene are often represented only from a single developmental stage or tissue type and, therefore, may represent only one of many alternative splicing events. The only two available rice ESTs for the synaptobrevin gene indicate failure to splice intron 2, resulting in a severely truncated protein. However, the highly conserved gene structure and protein similarity compared to the barley and Arabidopsis homologs indicates that either this gene is still properly spliced in other tissues or under other conditions in rice or the mutations leading to improper splicing have occurred so recently that homology has not yet been degraded. Gene prediction programs, which are reasonably accurate in locating genic regions, often fall short in discerning the intricacies of specific gene structure. The automated gene prediction of HvPG2 eliminated two entire exons, truncated a third, and generated a false start site. The automated prediction of the OsPG2 generated an additional exon and introduced a new intron, which altered the termination site of the gene. However, automated prediction was helpful in discerning the most probable start site in the absence of full-length ESTs with the Arabidopsis sequence as a guide. In both instances, predicted genes from the completely sequenced Arabidopsis and rice genomes proved a valuable tool for discerning gene structure.
Although some repetitive sequences are remnants of ancient insertion events, the vast majority of transposable element insertions occurred post speciation (SanMiguel and Bennetzen, 1998
A wide variety of small chromosomal rearrangements have occurred between the region containing Ha locus in barley and its colinear rice sequence (Fig. 3). An interchromosomal event concluded in the translocation of the putative chalcone synthase gene. Although at least three copies of ATPase were present within the colinear region in both species, sequence homology revealed a greater conservation among paralogs within the same species than between orthologs of the different species. This indicated a total of six different independent duplications involving one gene inversion post speciation. Three further gene duplications involving a minimum of one inversion also arose from the ancestral grain texture gene in the barley genome. An intrachromosomal rearrangement resulted in the repositioning of two conserved gene clusters. One of these gene clusters, GC2 (VAMP, GlcNAc, and GSP), has also been conserved in T. monococcum (Chantret et al., 2004
Several additional breaks in colinearity existed between the wheat and barley genomes. The rice and wheat sequences contained a putative gene just upstream of GC2, which was not present in the barley sequence (Chantret et al., 2004 A low level of microcolinearity still exists between the two grass species and Arabidopsis. The closest homologs to the putative N-acetylglucosaminyltransferase and ATPase are under 14 kb apart on chromosome 5 in reverse orientation and separated by one additional gene. In addition, the closest Arabidopsis homologs to PG1 and PG2 are located only 1 kb apart in similar orientation on chromosome 1. Although the closest homolog to the putative synaptobrevin gene was also located on chromosome 1 it was widely separated from this gene cluster.
Only two other studies have compared large orthologous regions from rice and barley at the sequence level. At the Xwg644 locus, despite one gene inversion and a single gene duplication in barley as compared to rice, the gene order of all four orthologs was completely conserved (Dubcovsky et al., 2001
The extent of the difference between rice and barley in the organization of this region could be related to the function of the grain texture genes. Selective pressure may have led to the maintenance of subsequent duplications of the ancestral copy and the gradual ascertainment of new functions within the gene family. It is unlikely that the currently accepted function of these genes, namely in controlling grain texture (for review, see Morris, 2002
BAC Selection
A set of 14 BACs (barley [Hordeum vulgare] cv Morex; Yu et al., 2000
Purified BAC DNA was obtained using the Qiagen Large Construct kit (Qiagen USA, Valencia, CA) and sheared by nebulization for 15 s at 10 pounds per square inch. The 2-kb and 5-kb fractions were blunt ended, dephosphorylated, and ligated into pUC18 cloning vector. Individual clones were sequenced in the forward and reverse direction using ABI big dye terminator chemistry and analyzed on an ABI 3700 automated capillary sequencer (ABI, Sunnyvale, CA). Preassembly and assembly analysis of the sequencing reads were performed by using PHRED version 0.020425.c and PHRAP version 0.990329 software (University of Washington, Seattle; Ewing and Green, 1998
Preliminary characterization of the sequenced barley and rice (Oryza sativa) regions was preformed using standard nucleotide-nucleotide (BLASTN; Altschul et al. 1997 Sequence data from this article have been deposited with the EMBL/GenBank data libraries under accession numbers AY643842 to AY643844.
We thank A. Kleinhofs and M. Morgante for preliminary work in BAC identification and fingerprinting, respectively. Received April 3, 2004; returned for revision July 28, 2004; accepted August 14, 2004.
1 This work was supported by the Scottish Executive Environment and Rural Affairs Department. 
2 Present address: Department of Vegetable Crops, University of California, Davis, CA 95616. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.044081. * Corresponding author; e-mail wpowel{at}scri.sari.ac.uk; fax 44–(0)1382–568590.
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ABSTRACT
RESULTS
HvATPase-1 pseudogene has maintained 84% and 91% nucleotide homology to HvATPase-2 and HvATPase-3, respectively, despite the insertion of the HORPIA-2_AY643843 retrotransposon and several insertion and deletion events causing shifts in the reading frame. Remnants of an additional ATPase gene (
