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DNA Research Advance Access originally published online on February 12, 2007
DNA Research 2006 13(6):267-274; doi:10.1093/dnares/dsm001
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© The Author 2007. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Identification and Mapping of Expressed Genes, Simple Sequence Repeats and Transposable Elements in Centromeric Regions of Rice Chromosomes

Hiroshi Mizuno1, Kazue Ito2, Jianzhong Wu1, Tsuyoshi Tanaka1, Hiroyuki Kanamori2, Yuichi Katayose1, Takuji Sasaki1 and Takashi Matsumoto1,*

1 National Institute of Agrobiological Sciences, 1-2 Kannondai 2-chome, Tsukuba, Ibaraki 305-8602, Japan
2 Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan

Received 2 November 2006; revised 14 January 2007


   Abstract
Top
 Abstract
1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Supplementary data
 Acknowledgements
 REFERENCES
 
The genomic sequences derived from rice centromeric regions were analyzed to facilitate the comprehensive understanding of the rice genome. A rice centromere-specific satellite sequence, RCS2/TrsD/CentO, was used to screen P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) genomic libraries derived from Oryza sativa L. ssp. japonica cultivar Nipponbare. Physical maps of the centromeric regions were constructed by DNA fingerprinting methods and the aligned clones were analyzed by end sequencing. BLAST analysis revealed the composition of genes, centromeric satellites and other repetitive elements, such as RIRE7/CRR, RIRE8, Squiq, Anaconda, CACTA and miniature inverted-repeat transposable elements. Fiber-fluorescent in situ hybridization analysis also indicated the presence of distinct clusters of RCS2/TrsD/CentO satellite interspersed with other elements, instead of a long homogeneous region. Several expressed genes, sequences representative of ancestral organellar insertions, relatively long simple sequence repeats (SSRs), and sequences corresponding to 5S and 45S ribosomal RNA genes were also identified. Thirty-one gene sequences showed high-similarity to rice full-length cDNA sequences that had not been matched to the published rice genome sequence in silico. These results suggest the presence of expressed genes within and around the clusters of RCS2/TrsD/CentO satellites in unsequenced centromeric regions of the rice chromosomes.

Key words: genome; FL-cDNA; centromere; transposon


   1. Introduction
Top
 Abstract
 1. Introduction
2. Materials and Methods
 3. Results and Discussion
 Supplementary data
 Acknowledgements
 REFERENCES
 
The centromere of a chromosome plays a key role during mitosis and meiosis. The centromeric region contains species-specific satellite sequences and various kinds of transposable elements1Go–6Go as well as genes.7Go These highly repetitive sequences complicate many aspects of genomic sequencing—including cloning, mapping, chromosomal walking and assembling the fragments of DNA sequences in silico—so that genomic sequencing of the centromeric regions of higher eukaryotes can be difficult. Therefore, the genes in centromeric regions could not be fully elucidated, even for the so-called completely sequenced genomes.8Go,9Go

Rice is considered to be a model monocot plant because of its relatively small genome size and its high-synteny with other cereal crops.10Go As the first step in the functional characterization of the rice genome, the International Rice Genome Sequencing Project (IRGSP) completed a high-quality map-based sequencing of the genome of Oryza sativa L. ssp. japonica cv. Nipponbare.11Go–15Go Even though it covers >95% of the estimated 390 Mb total genome sequence, the published rice genomic sequence includes the centromeric regions of chromosomes 4, 5 and 8, and only portions of the centromeric regions of the 9 remaining chromosomes. The overall sequence data corresponds to only 13% of the full set of rice centromeric regions.

The rice centromeric region consists mainly of repeats of 155–165 bp RCS2/TrsD/CentO satellite DNA and the centromere-specific retroelement RIRE7/CRR.16Go–21Go In addition to the repetitive elements, high-quality sequence data of the centromeres of chromosomes 4 and 8 revealed that genes are predicted to lie between and around the satellite sequences,16Go,17Go and 12 of these genes are expressed in leaf and root tissues.18Go Do other rice centromeric regions contain active genes? Although the Rice Genome Research Program (RGP) attempted to construct sequence-ready PAC/BAC physical maps of the centromeric regions, interference with repetitive sequences prevented further chromosomal walking and subsequent genomic sequencing of the regions.11Go

Here we describe a comprehensive analysis that identifies and maps centromeric sequences derived from the 12 rice chromosomes. We reveal the occurrence of expressed genes, organellar insertions, relatively long simple sequence repeats (SSRs), and ribosomal RNA genes in rice centromeric regions. In addition, we describe the composition and distribution of centromeric repetitive sequences. Finally, we evaluate our PAC/BAC library and discuss strategies that might be used to complete the genomic sequencing of rice centromeric regions.


   2. Materials and Methods
Top
 Abstract
 1. Introduction
 2. Materials and Methods
3. Results and Discussion
 Supplementary data
 Acknowledgements
 REFERENCES
 
2.1. PCR screening
PAC and BAC libraries were constructed from genomic DNA derived from the rice cultivar Nipponbare (JP 229579 in NIAS GenBank, Oryza sativa L. ssp. japonica) that was generated by the Rice Genome Research Program. PCR screening was performed as described previously.22Go We designed four sets of primers and selected the set that most efficiently amplified the RCS2/CentO/TrsD array from the DNA pools. We confirmed that we could use this primer set to obtain clones that had already been mapped by chromosomal walking.11Go,22Go DNAs from 192 PAC clones randomly selected from the library and 545 RCS2/CentO/TrsD-containing PAC/BAC clones were isolated using standard alkaline lysis procedure from 2 ml overnight cultures in Luria–Bertani (LB) medium containing kanamycin (40 µg/ml) or chloramphenicol (12.5 µg/ml). Insert sizes of these clones were determined by pulsed-field gel electrophoresis (PFGE). PAC/BAC DNAs were digested by NotI and separated in 1% agarose gels in 0.5x TBE at 6 V/cm with a 5–40 s pulse time for 14 h.

2.2. BAC/PAC end sequencing
The BAC and PAC clones were grown for 22 h with shaking. DNA of each BAC/PAC clone was prepared in a 96-well plate using a liquid-handling robot (Quadra 3, Tomtec, Hamden, CT, USA). Bacterial cells were harvested by centrifugation and lysed according to the standard alkaline lysis protocol. The insert DNA was purified using isopropanol precipitation, dissolved in deionized H2O and sheared into ~1 kb fragments by sonication (Sonifier 450, Branson, Danbury, CT, USA). Sequencing was performed using the Big Dye terminator reaction mix (ABI, Foster City, CA, USA) on ABI3700 capillary sequencers (ABI). Repetitive elements were identified by BLAST analysis using the TIGR repetitive sequences library (http://www.tigr.org/tdb/e2k1/osa1/blastsearch.shtml). Sequence similarity search was performed against the rice full-length complementary DNA (FL-cDNA) sequences23Go,24Go including previously unmapped sequences (identity <95%, total coverage <90%).

2.3. DNA fingerprinting
Agarose-gel-based fingerprinting methodology25Go was used to generate HindIII fingerprints of PAC/BAC clones. PAC/BAC DNAs were isolated using a REAL kit (Qiagen, Hilden, Germany) and then digested with HindIII. The restriction digestion fragments were electrophoresed in 1.2% agarose gels. The gels were then stained with SYBR Green I (Invitrogen, Carlsbad, CA, USA). Positions of DNA bands on the gel images were identified using the program Image25Go and checked manually. DNA fragments derived from vector DNA (one fragment from pBeloBAC11 or four fragments from pCYPAC2) were removed manually. Fingerprints derived from PAC/BAC clones in pericentromeres were integrated to determine the chromosomal location of each contig. The initial fingerprint assembly was performed automatically using fpc V4.725Go–27Go at a Sulston score cut-off of E–12 and a tolerance of 2. To correct errors, the contigs were edited manually at cutoff of E–8 to E–13 and a tolerance of 2.

2.4. Genetic mapping
Genetic mapping was performed according to previously published methods28Go with minor modifications. In brief, after a BLAST search against the TIGR rice repeat database and the RGP genomic sequence database, unique sequences were selected. Rice molecular linkage map using 186 F2 plants derived from a single cross between the japonica cultivar Nipponbare and the indica cultivar Kasalath was used.

2.5. Fluorescence in situ hybridization (FISH)
Fiber-FISH analysis was performed according to previously published methods29Go with minor modifications. PCR fragments amplified from centromere specific repeats or retrotransposon sequences in the centromeric region of chromosome 8 were used as DNA probes. DNA fragments of ~5 kb were amplified by PCR and then mixed to make a DNA probe for retrotransposons. Probes were labelled with digoxigenin- or biotin-labelled dUTP and detected with a fluorescein isothiocianate-conjugated anti-digoxigenin antibody or Cy3-conjugated avidin. All fluorescent images were captured using a fluorescence microscope (BX51, Olympus, Tokyo, Japan) with a charge-coupled device camera (CoolSNAP HQ, Roper Scientific, Tucson, AZ, USA).


   3. Results and Discussion
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
Supplementary data
 Acknowledgements
 REFERENCES
 
3.1. Screening of PAC/BAC clones that cover the 12 centromeric regions of rice
In this work we sought to comprehensively screen PAC/BAC clones from the 12 rice centromeric regions. Because all rice centromeres contain centromere-specific tandem repeats, RCS2/TrsD/CentO satellite sequences,19Go we screened the two rice genomic libraries using RCS2/TrsD/CentO as a probe. We obtained a total of 545 clones—398 PAC clones and 147 BAC clones, which correspond to 0.57 and 0.30% of the total clones in the PAC and BAC libraries, respectively (Table 1).


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  		Table 1. Centromeric PAC/BAC clones

 
In addition to the RCS2/TrsD/CentO satellite sequence, other rice centromere-specific motifs include the RCH1, RCH2, RCH3 and RCS1 sequences.19Go Though we screened both the PAC and BAC libraries with these sequences, only four positive clones in total were obtained (data not shown). Because these retrotransposon-derived centromeric sequences may demonstrate high-diversity,17Go,20Go they seem to be unsuitable as probes for overall screening of rice centromere-specific clones.

3.2. Composition and structure of repetitive sequences in rice centromeric regions
We analyzed the sequence of both ends for a total of 545 rice centromere-specific clones (Supplementary Table 1). BLASTN analysis using various databases revealed the composition of centromere sequences. The analysis identified the RCS2/TrsD/CentO satellite sequence and various repetitive elements, including RIRE7/CRR, RIRE8, Squiq, miniature inverted-repeat transposable elements (MITEs), Anaconda and CACTA, in rice centromeric regions (Table 2). The RCS2/TrsD/CentO satellite accounted for 34.7% of the total region sequenced in this study, and RIRE7/CRR, a centromere-specific Ty3/gypsy type retroelement of rice,20Go,21Go accounted for 14.9% (Table 2). Thus, these 2 centromere-specific repetitive elements comprised 49.6% of the sequenced region. The MITE family30Go,31Go accounted for 12.7% of the total region sequenced (Table 2). MITEs have a pronounced bias toward euchromatic regions11Go,13Go,14Go and are considered to be associated with genes.32Go,33Go This propensity suggests that genes might be present near the MITEs in rice centromeric regions.


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  		Table 2. Distribution of sequence motifs in rice centromeres

 
A cytogenetic approach was applied to analyze the structure of these repetitive sequences. Fiber-FISH analysis using RCS2/TrsD/CentO and three repetitive sequences we described in Table 2 as probes indicated that RCS2/TrsD/CentO sequences are arranged in discrete clusters, instead of being distributed uniformly throughout the centromeric region of rice (Fig. 1A). This result is somewhat contrary to the previous finding from pachytene FISH analysis,21Go but recent sequence analysis from rice chromosomes 416Go and 817Go,18Go supports our finding. The repetitive elements RIRE3, RIRE7/CRR and RIRE8 seem to be dispersed throughout centromeric regions, with no obvious clustering (typical images, Fig. 1B–D). Fiber-FISH analysis illustrates the complex structure of rice centromeric regions and supports previous estimates regarding their composition in Table 2.


Figure 1
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  		Figure 1. Structure of the centromeric region revealed by FISH analysis of extended DNA fibers (fiber-FISH). Typical fluorescent images from DNA fibers probed with RCS2/TrsD/CentO (green, A–E) and various repetitive sequences (red)-RIRE3 (B), RIRE7/CRR (C), RIRE8 (D), and 5S rDNA (E)-are shown. Scale bar, 5 µm.

 
3.3. Identification of expressed genes, SSRs and organellar insertions in rice centromeric regions
To identify expressed genes in rice centromeric regions, we conducted a sequence similarity search between the end sequences of the screened PAC/BAC clones and rice full-length cDNA (FL-cDNA) sequences23Go,24Go in silico. BLASTN analysis indicated that 31 end sequences had high-similarity (E value < E–05) to rice FL-cDNA sequences with no match to published rice genome sequences in silico (Table 3). These results suggest that genes are present and expressed in unsequenced centromeric regions of the rice chromosomes. Whereas the putative proteins encoded by 11 FL-cDNA sequences were similar to various types of known proteins, such as ribose-phosphate diphosphokinase, urease and transcription factors, those encoded by the remaining FL-cDNA sequences had no pronounced similarity to any known protein (Table 3). We searched genes in Arabidopsis thaliana, which had sequence similarity with rice centromeric genes described in Table 3 by using MIPS (Munich Information center for Protein Sequences). Sixteen rice genes had sequence similarity with those in A.thaliana but 15 rice genes had no similarity (data not shown). These 16 genes were not located in the centromeric regions of A.thaliana, indicating that the chromosomal location of these genes is different between rice and A.thaliana.


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  		Table 3. BLAST analysis of genes at rice centromeres

 
We identified SSRs in rice centromeric regions. Among the 47 distinctive motif families of rice SSRs,11Go only the AT motif had been found in centromeres (Table 2). It is interesting that although the AT motif in centromeric region was repeated more than 200 times (Supplementary Table 1) only 2 loci with >200 AT repeats had previously been identified among the 18 828 SSR loci in the rice genome,11Go suggesting that AT repeats might be relatively long in centromeric regions for the rice genome overall.

The sequences we identified also include data suggestive of insertion of ancestral organellar DNA in the rice nuclear genome. P0698F05_F is similar to the DNA sequence that encodes mitochondrial NADH dehydrogenase subunit 1 (Supplementary Table 1). This result suggests that mitochondrial insertions occur even in centromeric regions and similar organellar insertions account for 0.18–0.19% of the published nuclear genome of rice.11Go

3.4. Mapping of PAC/BAC sequence data, genes and repetitive sequences
We constructed clone-based physical maps of the 12 rice centromeric regions. A total of 545 centromere-specific clones and 42 selected clones (position markers, Supplementary Table 2) were subjected to DNA fingerprinting analysis to make contigs. Contigs were mapped to a specific centromeric region if they contained marker clones. The locations of four newly mapped PAC/BAC sequences corresponded to genetically identify centromeric regions of the 12 rice chromosomes. In total, 13 contigs and 4 clones were mapped genetically or in silico (Supplementary Figure 1), corresponding to 2.98 Mb of the 12 rice centromeric regions. In addition, 2 contigs totaling 360 kb in size have not been anchored yet, and 2 FL-cDNA sequences (AK067951 [GenBank] , AK063425 [GenBank] ) belonged to unmapped contigs (Table 3, Supplementary Figure 1). Our findings suggest that these contigs might exist as gene-containing islands in centromeric regions.

After we mapped the 13 contigs, we then mapped the genes and transposable elements described in section 3.2. Mapping the 13 contigs allowed us to map the genes and transposable elements described earlier to their respective chromosomes in silico so there was no need to map each gene or motif individually (Table 4). In addtion to the repetitive elements, the 5S rDNA genes were mapped on chromosome 11 (Table 4). It was previously reported that the 5S rDNA cluster lies close to the centromeric region on the short arm of chromosome 11.34Go We confirmed the presence of the single long cluster of 5S rDNA near the RCS2/TrsD/CentO cluster by using fiber-FISH and found that the gap between these 2 clusters is <50 kb (Fig. 1E). The 45S rDNA consisting of 17S, 5.8S and 25S rDNA coding units was identified on chromosome 1 (Table 4). However, fiber-FISH and mitotic FISH both failed to identify the 45S rRNA cluster near the RCS2/TrsD/CentO satellite (data not shown); the 45S rDNA cluster previously had been detected at the end of the short arm of chromosome 9.35Go Our finding suggests that 45S rDNA sequences are not clustered but are dispersed or fragmented in the centromeric region.


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  		Table 4. Chromosomal location of repetitive sequences in rice centromeric regions

 
We encountered difficulty in constructing a complete physical map using PAC/BAC clones because the clones only minimally extended the contigs that had been constructed by chromosomal walking. Overall, 71% (427 of 598) of the PAC/BAC clones have not been mapped because they contain too few DNA fragments to facilitate assigning into contigs by DNA fingerprinting methods (Supplementary Figure 2). The distribution of insert length indicates that 47.2% (188 of 398) of centromeric PAC clones have inserts <60 kb (Fig. 2), compared with 13.6% in the total library.36Go Moreover 10.3% (41 of 398) of PAC clones seem to have no insert (data not shown). This finding suggests that inserts containing repetitive sequences are easily deleted from PAC clones, as we also experienced when we constructed genomic libraries in YAC vector (unpublished data). Thus it may be necessary to use more efficient cloning vectors to obtain genomic clones containing the overall centromeric region of rice.


Figure 2
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  		Figure 2. Size distribution of RCS2/TrsD/CentO-containing PAC/BAC clones, plotted as ratio of clones (%) versus insert size (kb).

 
3.5. Toward the complete identification of genes in centromeric regions
In this study, we obtained PAC/BAC clones and constructed a partial physical map of unsequenced rice centromeric regions (Supplementary Figure 1), which could be useful for analysis of the centromeres by clone-by-clone genomic sequencing and subsequent prediction of genes. Comparison between the end sequences of the PAC/BAC clones and sequences of rice FL-cDNAs (Table 3) suggested that expressed genes exist within and around the RCS2/TrsD/CentO clusters in the centromeric regions. Previous studies have also identified new genes in the centromeres of choromosomes 416Go and 8,17Go,18Go and our current findings suggest that other rice centromeric regions contain many more expressed genes. An overall comparison between the published rice genome sequence and total rice FL-cDNAs was conducted recently and showed that 2257 of 28 469 FL-cDNA sequences do not match the rice genome,24Go suggesting that the unsequenced regions, especially centromeric regions, contain many genes. The centromeric PAC/BAC clones we have identified may be used as probe for DNA microarrays comprising the entire set of FL-cDNAs in order to provide further insights into expressed genes in rice centromeric regions. In our strategy, however, we detected genes with evidence of expression, and we did not consider genes without transcriptional evidence. In addition, genes silenced by DNA methylation may also exist due to the flanking repetitive sequences/transposons in the centromeric region.

It is important to note that our discussion is limited to the centromeric regions represented by the PAC/BAC clones we obtained. Although we tried to analyze rice centromeric sequences comprehensively, the sequences we obtained in this study may not completely cover the entire rice centromeric region. The percentage of RCS2/TrsD/CentO in the rice genome data is ~1.8% (6.9 of 390 Mb) according to an estimate based on the signal intensity of RCS2/TrsD/CentO satellites in FISH analysis21Go but only 0.46% in the PAC/BAC libraries used here (Table 1). This suggests that the PAC/BAC clones obtained is insufficient to cover the overall rice centromeric region. In addition, we sequenced only the ends of the clones. Because the average read length was 536 bp after trimming of the vector sequence, a total of 0.58 Mb (including redundancy) was sequenced, corresponding to 8.4% (0.58 of 6.9 Mb) of the estimated length of the 12 rice centromeric regions.

Complete genomic sequencing of the remaining centromeric regions, which are composed mainly of repetitive elements, clearly presents a considerable challenge. We consider that almost all remaining regions, typically long clusters of RCS2/TrsD/CentO satellites (Figure 1), would not be clonable because they contain few restriction enzyme sites and because the clones would be unstable in Escherichia coli (Fig. 2). Therefore, PAC/BAC clone-based sequencing and other essentially different methods for genome analysis, such as fiber-FISH, is likely needed to be used in concert to achieve a strategy that will be effective in completely characterizing the 12 rice centromeric regions.


   Supplementary data
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Supplementary data
Acknowledgements
 REFERENCES
 
Supplementary data are available online at www.dnares.oxfordjournals.org.


   Acknowledgements
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Supplementary data
 Acknowledgements
REFERENCES
 
The authors thank Dr B. A. Antonio for critical reading of the manuscript. This work was supported by Grants-in-Aid for Scientific Research for Young Scientists (B) 17710165 from the Ministry of Education, Culture, Sports, Science and Technology of Japan to H.M., and grants GD-2007 from the Ministry of Agriculture, Forestry and Fisheries of Japan.


   Footnotes
 
*To whom correspondence should be addressed. Tel: +81 29 838 7441, Fax: +81 29 838 7468, E-mail: mat{at}nias.affrc.go.jp

Communicated by Satoshi Tabata


   REFERENCES
Top
 Abstract
 1. Introduction
 2. Materials and Methods
 3. Results and Discussion
 Supplementary data
 Acknowledgements
 REFERENCES
 

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H. Mizuno, J. Wu, Y. Katayose, H. Kanamori, T. Sasaki, and T. Matsumoto
Chromosome-Specific Distribution of Nucleotide Substitutions in Telomeric Repeats of Rice (Oryza sativa L.)
Mol. Biol. Evol., January 1, 2008; 25(1): 62 - 68.
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