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Genetics, Vol. 172, 2529-2540, April 2006, Copyright © 2006
doi:10.1534/genetics.106.055772
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,1
,**,2
* Department of Plant Breeding and Genetics, Department of Plant Biology, Boyce Thompson Institute for Plant Research and ** U.S. Department of Agriculture–Agricultural Research Service, Plant, Soil, and Nutrition Lab, Cornell University, Ithaca, New York 14853 and Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
2 Corresponding author: Department of Plant Breeding and Genetics, 248 Emerson Hall, Cornell University, Ithaca, NY 14853.
E-mail: sdt4{at}cornell.edu
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ABSTRACT |
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 TOP ABSTRACT MATERIALS AND METHODSRESULTS AND DISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10–100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin—the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently—well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.
Advances in the genomic sequencing of model plants and animals have provided great insight into the composition and organization of genes in euchromatin as well as the structure and function of the heterochromatin. The Ty3/Gypsy class retrotransposons and their relatives have been found in pericentromeric regions, especially in grasses (CHENG et al. 2002; JIANG et al. 2003; MROCZEK and DAWE 2003; WU et al. 2004). Tandem repeats and retroelements are also keys for centromere recognition by kinetochore proteins. Repeats in the pericentromeric regions also play important roles in sufficiently initiating the recruitment of histone modification enzymes and promoting the formation and maintenance of heterochromatin by RNAi machinery (CHENG et al. 2002; HALL et al. 2002; VOLPE et al. 2002; ZHONG et al. 2002; BENDER 2004; SUN et al. 2004). This still leaves open several important questions: What are the global differences between euchromatin and heterochromatin? Which of these differences are consistent among species and which are species specific? What evolutionary forces have molded the composition and function of heterochromatin vs. euchromatin? In hopes of shedding light on these questions, we have conducted a series of molecular cytogenetic experiments to characterize the nature of heterochromatin vs. euchromatin in the model crop plant—tomato.
The tomato (Solanum lycopersicum) is a diploid species with a genome composed of 12 chromosomes (2n = 2x = 24) totaling 950 Mb of DNA (ARUMUGANATHAN et al. 1991). Along with maize, it was an early model system for genetics and cytogenetics studies in plants (for review, see RICK 1971). Like many other plant species, such as Arabidopsis and Medicago truncatula, tomato chromosomes contain long, contiguous stretches of euchromatin at the distal ends of most chromosomes and heterochromatic regions flanking the centromeres (DE JONG 1998; KULIKOVA et al. 2001; FRANSZ et al. 2003). Approximately 25% of the tomato genome is contained in the euchromatin and 75% is contained in the pericentromeric heterochromatin (PETERSON et al. 1998). Although much work has been done on Arabidopsis, which has relatively little heterochromatin, tomato would be more similar to the majority of plants, with less known on the global organization of euchromatin and heterochromatin, especially crop plants that have large genomes and more heterochromatin. We report herein the annotation of 11 sequenced BAC clones assigned, via in situ hybridization, to both euchromatin and heterochromatin. From a comparative analysis of these BACs emerges a general picture of the global organization and evolution of euchromatin vs. heterochromatin in this model dicot plant species.
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MATERIALS AND METHODS |
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Identifying highly repetitive sequences in BACs:
The 11 sequenced BAC clones were computationally screened for repetitive elements in two ways. First, each was compared against two repeat databases: Solanaceae repeat database, which contains all known repeats from solanaceous species, and Repbase, which is a comprehensive database of repetitive element consensus sequences in eukaryotic genomes, including transposable elements (TEs) and tandem repeats of diverse origins (JURKA 2000; OUYANG and BUELL 2004). If the gene model was homologous with known TEs (TIGR_Sol_repeat, or Repbase repeats, or Arabidopsis TEs), then it was annotated as a TE-related gene. Second, the BACs were computationally screened against each other (blastn; E-value <10–20 and bits score >100) in an effort to identify repetitive sequence motifs shared by two or more BACs. Segments of BACs containing putative repetitive elements were aligned and manually examined in an effort to determine the length and boundaries of each repetitive element.
Southern hybridization:
A subset of the repetitive elements identified in this study was screened against the genomes of other solanaceous species to determine the taxonomic distribution of these elements. For these studies, PCR-amplified repeats were amplified, labeled with 32P, and used as probes on the genomic Southern blots containing restriction-digested genomic DNA from S. pimpinellifolium L. (LA1589), S. chmielewskii (C. M. Rick, E. Kesicki, J. Fobes, M. Holle, D. M. Spooner, G. J. Anderson, and R. K. Jansen) (LA1316), S. peruvianum L. (LA1708), S. chilense (Dunal) Reiche (LA1959), S. pennellii Correll (TA56), S. neorickii (D. M. Spooner, G. J. Anderson, and R. K. Jansen) (LA2133), S. habrochaites (S. Knapp and D. M. Spooner) (LA1777), S . lycopersicum L. (TA209), S. tuberosum L., Capsicum annuum L. (garden pepper), Petunia x hybrida hort. ex E. Vilm., and S. melongena L. (eggplant) (SPOONER et al. 2005). Blots were hybridized at 60° and washed in 2x SSC for 20 min and in 1x SSC for 10 min. The tomato 45S rDNA (R45S) ribosomal gene probe was used as a positive control for estimating the relative strength of hybridization signals (GANAL et al. 1988).
For estimating the methylation status of cytosine in the retrotransposons, a Southern blot was made using tomato (TA56 and TA209) genomic DNA digested with methylation-sensitive restriction enzymes, HpaII and EcoRI, and methylation insensitive isoschizomers, MspI and BstNI (MESSEGUER et al. 1991). The LTR and polyprotein regions of the retrotransposon were labeled with 32P-dCTP and used as probes on the genomic Southern blots. Since cytosines in the tomato chloroplast are not methylated, PCR fragments of tomato chloroplast genes (AY216521, AF397080, and AF263101) were used as the methylation negative control (FOJTOVA et al. 2001).
Genetic mapping:
DNA fragments were amplified from each BAC clone using primers designed from annotated exons or BAC ends and then mapped as cleaved amplified polymorphic sequence or RFLP markers onto the high-density tomato map on the basis of a population of 80 F2 individuals from the cross S. lycopersicum LA925 x S. pennellii LA716 (FULTON et al. 2002; http://www.sgn.cornell.edu/cgi-bin/mapviewer) (supplemental Table 1 at http://www.genetics.org/supplemental/).
Copy number reconstruction experiments:
To estimate the copy numbers of the tomato repetitive sequences, PCR products representing the repeats were used in the reconstruction experiments. Denatured tomato genomic DNA extracted from S. lycopersicum cv. TA209 (400 and 1000 ng) was spotted onto Hybond N+ membrane (Amersham, Arlington Heights, IL) according to GANAL et al. (1988). Different quantities of PCR product, representing different copy numbers of the repeat in the tomato genome, were also spotted on the same membrane. Hybridization of the 32P-dCTP-labeled repeats, analysis of the autoradiographs, and estimation of the copy number, from a plot of densities vs. copy numbers, were carried out as described by BERNATZKY and TANKSLEY (1986). The mean results of three independent reconstruction estimates were reported for each repeat.
Pachytene chromosome preparation and fluorescence in situ hybridization:
Immature tomato flower buds, 3 mm in length, were harvested and fixed in Carnoy's solution (3:1 ethanol:glacial acetic). Anthers containing pachytene stage microsporocytes were squashed in acetocarmine solution. Slides were frozen in liquid nitrogen, with coverslips removed, dehydrated through a series of ethanol washes (70, 90, and 100%), and subjected to fluorescence in situ hybridization (FISH) using the method of JIANG et al. (1995). DNA of individual BACs was isolated using a standard alkaline extraction and labeled by nick translation with digoxigenin-16-dUTP (Roche Diagnostics, Indianapolis). Slides with meiotic chromosomes were denaturated at 80° for 2 min in a buffer containing 70% formamide in 2x SSC and immediately placed in a series of precooled ethanol baths (70, 90, and 100%, for 5 min each). Denaturated probe mixture (20 µl containing 50–100 ng labeled probe, 2x SSC, 50% deionized formamide, and 10% dextran sulfate) was applied to each slide and covered with a coverslip. Hybridization was carried out at 37° overnight in a humid chamber. After removing the coverslips, slides were washed in 2x SSC at 42° for 10 min and 2x SSC at room temperature for 5 min. Biotin-labeled probes were detected by fluorescein isothiocyanate (FITC)-conjugated sheep-antidigoxigenin antibody (Roche Diagnostics). Chromosomes were counterstained with 4',6-diamidino-2-phenylindole (DAPI) in an antifade solution (Vector Laboratories, Burlingame, CA). Chromosomes and FISH signal images were captured using an Olympus BX61 fluorescence microscope with a micro-CCD camera. Grayscale images were captured for each color channel and then merged using Image-Pro Plus software.
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RESULTS AND DISCUSSION |
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TOPABSTRACTMATERIALS AND METHODSRESULTS AND DISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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The fully sequenced genomes of Arabidopsis and rice provide reference points with which to compare the organization of tomato euchromatin and heterochromatin. For all three species, the estimated nontransposon (non-TE) gene densities for euchromatin are remarkably similar: tomato, 6.7 kb/gene; Arabidopsis, 4.5 kb/gene; and rice, 6.9 kb/gene (COPENHAVER et al. 1999; KUMEKAWA et al. 2001; JIAO et al. 2005). However, striking differences are revealed in the heterochromatin. Rice heterochromatin has gene density only slightly lower than the gene density in euchromatin (11 kb/gene, JIAO et al. 2005). In contrast, Arabidopsis and tomato heterochromatin have non-TE gene densities dramatically lower than that in euchromatin: Arabidopsis, 256 kb/gene on chromosomes 2 and 4; and tomato, >56 kb/gene (COPENHAVER et al. 1999). As already noted, the higher gene density estimate for tomato heterochromatin (in comparison with Arabidopsis) may reflect a bias in the tomato estimate due to the nonrandom sampling of heterochromatic BACs (see previous section).
The tomato genome is composed of 950 Mb of DNA, 25% of which is euchromatin (ARUMUGANATHAN et al. 1991; DE JONG 1998; PETERSON et al. 1998). Thus, at a gene density of 6.7 kb/gene, we estimate that the euchromatin contains 35,440 genes. On the basis of a large EST database, the entire tomato genome has been previously estimated to encode 35,000 genes (VAN DER HOEVEN et al. 2002). Thus the euchromatin is sufficient to encode most of tomato non-TE genes. The remaining 75% (712 Mb) of the tomato genome is composed of heterochromatin. If the heterochromatin contains 1 gene every 56 kb, one would estimate that the heterochromatin contains 12,700 genes and that the tomato genome contains a total of 48,000 genes, which is dramatically higher than the estimate from the EST data. This discrepancy is likely due to the biased estimate of the heterochromatic gene density (see previous section). If the unbiased heterochromatin non-TE gene density from Arabidopsis (256 kb/gene) is used for the estimation, the tomato heterochromatin would be predicted to contain only 2800 genes. This would also lead to a predicted gene content of 38,240 genes in the tomato genome (35,440 in the euchromatin + 2800 in the heterochromatin)—a value much closer to that predicted from EST data (VAN DER HOEVEN et al. 2002). If these estimates are valid, then the tomato heterochromatin, which comprises 75% of the tomato nuclear genome, likely accounts for <10% of the non-TE genes—an important observation to be taken into account when contemplating sequencing of the genome of tomato or other solanaceous species (see next section).
Repeat composition of heterochromatin vs. euchromatin:
In an effort to identify repeat elements in the tomato genome, all BAC sequences were compared with each other using blastn. A sequence element was classified as a "repeat" if it was shared by two or more BAC clones. Using this criterion, a total of three distinct repeat families were identified, Jinling, LARD1, and LARD2, involving five different BACs—all assigned to the heterochromatin (Table 1). No shared repeats were identified in the euchromatic BACs (Table 1).
Tom-LARD1 and Tom-LARD2:
Two repeat families associated with retrotransposons (deemed large retrotransposon derivatives, LARDs) (KALENDAR et al. 2004) were identified due to the hallmarks of long terminal repeats (LTRs), ranging from 750 to 1100 bp. LARD1 and LARD2 had two- and three-member elements, respectively. The sizes of the internal sequences of LARD1 and LARD2 elements varied from 2 to 5 kb, but none of them contained any coding sequences, and hence they are not likely to be functional elements. Elements in the same family only share sequence similarity in the LTRs, but not in the internal noncoding sequences, suggesting that LARDs are nonautonomous retroelements.
LTRs at opposite ends of each Tom-LARD1 and Tom-LARD2 element shared 90–96% identity (sequence alignments are in the supplemental material at http://www.genetics.org/supplemental/). A comparison of orthologous, noncoding intergenic nuclear DNA segments from tomato and potato has revealed a sequence identity of 86% (Y. WANG, unpublished data for BAC comparison). Using this value and assuming that the transposon elements had identical LTRs upon insertion, we estimate that these LARDs integrated into their existing sites after the divergence of tomato and potato—an event estimated to have occurred 10 MYA (CHAW et al. 1997; WIKSTROM et al. 2001).
Jinling—a high-copy retrotransposon family preferential to tomato pericentromeric heterochromatin:
A third repeat family was identified that contains 15 elements (Table 1). The elements were found in multiple copies in five of the six BACs assigned to heterochromatin and hence may represent an abundant and heterochromatin-preferential repeat. On the basis of alignments and annotation of the 15 repeat members, this element is deduced to be a member of the Ty3/gypsy retrotransposon family and to share homology (84% identity) with the LTRs of two pericentromeric retrotransposon (PCRT)1a elements reported by YANG et al. (2005) (Figure 2A; SU and BROWN 1997; MARIN and LLORENS 2000) (data not shown). Eight of the 15 members appear to be complete, containing all of the structural and coding elements predicted for the Ty3 retrotransposon family. However, none of these elements appear to be capable of autonomous transposition since one or more of the coding regions always contained premature stop codons. A complete element from BAC 40B13 is annotated to comprise 8.8 kb, including 2-kb LTRs, two reverse transcriptase (RT) domains, and one integrase (IN) domain (Figure 2A, supplemental Table 1 at http://www.genetics.org/supplemental/). All but one member in BAC 2O7 also lack the GAG domain found in many other Ty3 retrotransposons. The LTRs of this retrotransposon family also show homology (80% identity) with a previously described tomato repeat—tomato genome repeat II (TGRII) (GANAL et al. 1988). The TGRII repeat family was determined to consist of >4000 member repeats, making it the highest-copy, interspersed element in the tomato genome (GANAL et al. 1988). On the basis of the high level of homology, we propose a family name of Jinling (meaning "golden bell" in Chinese and indicating the heterochromatin vicinity) to represent all the related elements reported herein as well as the previously reported PCRT1a and TGRII elements (GANAL et al. 1988; YANG et al. 2005).
Copy number of Jinling:
The copy number of Jinling in the tomato genome was estimated via a genomic reconstruction experiment using various components of the Jinling element from BAC 40B13 as probes (supplemental Table 1 at http://www.genetics.org/supplemental/). The results indicate that the tomato genome contains 2080, 1800, 1120, and 1450 copies of the LTR, RT, GAG, and IN domains, respectively. Thus, on the basis of Southern hybridization, we estimate a minimum of 2000 Jinling elements in the tomato genome. Previous reports had estimated that TGRII is present in 4000 copies (GANAL et al. 1988). The discrepancy in these estimates may be due to the fact that TGRII shows 80% homology with the canonical Jinling element. This level of sequence divergence is nearing the limits of detection by Southern hybridization. Thus, it is likely that additional, more diverged, copies of the Jinling element were not detected by the Southern reconstruction experiments described herein. Using 2000 and 4000 as the upper and lower copy-number limits and 8.8 kb as the upper size limit, we estimate that Jinling comprises 17.5–35 Mb of genomic DNA in the tomato genome (or 2.5% of the heterochromatin). Thus, Jinling is the largest family of retrotransposons thus far identified in the tomato genome and is apparently specific to the pericentric heterochromatin.
Jinling is nonrandomly distributed in pericentromeric heterochromatin:
While Jinling is apparently specific to the heterochromatin, it is not necessarily uniformly distributed throughout the heterochromatin. To address this issue, various domains of the Jinling element (LTR, RT, IN, and GAG) as well as TGRII (GANAL et al. 1988) were used as probes for FISH on tomato pachytene chromosomes. The results show that all probes hybridized almost entirely to pericentromeric heterochromatin—a result consistent with FISH experiments conducted with complete BACs containing Jinling (Figures 1 and 3). However, nonuniform hybridization signals suggest that Jinling may not be randomly distributed in the heterochromatin (Figure 3). To further investigate this possibility, the Jinling LTR and the entire TGRII elements were used as probes on tomato BAC filters of the HindIII library (BUDIMAN et al. 2000). If evenly distributed in the heterochromatin, one Jinling element would be predicted every 240 kb (using a 3000-copy-number estimate and 710 Mb of pericentric heterochromatin—see previous section). Considering an average BAC insert size of 120 kb one would predict that 37% of heterochromatic BAC clones (28% of all BACs) would contain at least one Jinling element. However, actual hybridization results indicated that only 13% of the BACs contain Jinling elements—a result consistent with Jinling occurring in nonrandom clusters in the heterochromatin. However, we cannot rule out the possibility that the BAC library is not biased against heterochromatic clones that are more likely to be rich in repeat elements. However, to further test the hypothesis that Jinling is not randomly distributed in the heterochromatin, the frequency and distribution of Jinling in the six heterochromatic BACs was tested against a uniform distribution model using the Kolmogorov–Smirnov test of uniform distribution. Using this test, we could reject the hypothesis that Jinling is randomly distributed across the six sequenced heterochromatic BACs (P < 0.001). This clustering effect may be caused in part by localized movement of Jinling (see next section).
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LTRs at the opposite ends of Jinling members share sequence similarities ranging from 90 to 97%. Considering the intergenic sequence identity of 86% between tomato and potato (Y. WANG, unpublished data), these results indicate that Jinling spread throughout the tomato heterochromatin subsequent to the divergence of tomato and potato from their last common ancestor—estimated to be 10 MYA (CHAW et al. 1997; WIKSTROM et al. 2001). Moreover, an unrooted tree suggests that the Jinling LTRs began diverging from each other at a very similar time (Figure 4). Using neutral substitution rates reported by NESBITT and TANKSLEY (2002), we estimate that Jinling began spreading throughout the tomato genome from 5 MYA—a period corresponding to the radiation of the Solanum tomato clade (formerly Lycopersicon) containing tomato and its closely related wild species (MILLER and TANKSLEY 1990; NESBITT and TANKSLEY 2002). Thus, Jinling elements are young TEs in the tomato genome, similar to the Dasheng elements found in the rice centromeric regions (JIANG et al. 2002).
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5 MYA—well after the divergence from potato and other solanaceous species that lack this element. However, the fact that tomato and other solanaceous species have very similar chromosome architecture with respect to euchromatin and pericentromeric heterochromatin raises the possibility that heterochromatin regions in these species are occupied by other retrotransposon families, which are common to all Solanaceae and might have radiated at different times during Solanaceae evolution (GOTTSCHALK 1954). The fact that pericentromeric heterochromatin appears to be deficient in genes and is evolving rather rapidly with respect to repeat composition may explain why chromosome pairing and meiotic recombination are often repressed (up to 1000-fold) in heterochromatin vs. euchromatin—especially in interspecific hybrids (TANKSLEY et al. 1992).
Implications of this study to the sequencing of the tomato genome and the genomes of other solanaceous species:
The results from this study indicate that as much as 90% of the estimated 38,000 nonretrotransposon genes in tomato can be discovered by sequencing the tomato euchromatin, which accounts for only 25% of the total DNA. Moreover, the high gene density and the lack of repetitive sequences should make computational assembly of euchromatin sequences relatively straightforward. Currently, an international project to sequence the tomato euchromatin on a BAC-by-BAC basis is being conducted by a consortium of 10 countries (http://www.sgn.cornell.edu/). Because of the low gene density, sequencing the 75% of the genome comprising heterochromatin would be expensive and may result in discovery of a relatively small fraction of genes. The small portion of genes embedded in the heterochromatin could be more efficiently discovered through EST databases (currently >500,000 ESTs exist for tomato and related solanaceous species; http://www.sgn.cornell.edu/) and/or methyl filtration sequencing (PALMER et al. 2003; BEDELL et al. 2005). Finally, because of the high level of conserved chromosomal macrosynteny and microsynteny among the genomes of solanaceous species, the sequence of the tomato euchromatin could be utilized in genetic/genomic studies across the entire family (DOGANLAR et al. 2002; PARAN et al. 2004; Y. WANG, unpublished data).
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ACKNOWLEDGEMENTS |
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FOOTNOTES |
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LITERATURE CITED |
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TOPABSTRACTMATERIALS AND METHODSRESULTS AND DISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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ARUMUGANATHAN, K., J. P. SLATTERY, S. D. TANKSLEY and E. D. EARLE, 1991 Preparation and flow cytometric analysis of metaphase chromosomes of tomato. Theor. Appl. Genet. 82: 101–111.
BEDELL, J. A., M. A. BUDIMAN, A. NUNBERG, R. W. CITEK, D. ROBBINS et al., 2005 Sorghum genome sequencing by methylation filtration. PloS Biol. 3: 103–115.
BENDER, J., 2004 Chromatin-based silencing mechanisms. Curr. Opin. Plant Biol. 7: 521–526.[CrossRef][Medline]
BENNETZEN, J. L., K. SCHRICK, P. S. SPRINGER, W. E. BROWN and P. SANMIGUEL, 1994 Active maize genes are unmodified and flanked by diverse classes of modified highly repetitive DNA. Genome 37: 565–576.[Medline]
BERNATZKY, R., and S. D. TANKSLEY, 1986 Majority of random cDNA clones correspond to single loci in the tomato genome. Mol. Gen. Genet. 203: 8–14.[CrossRef]
BORODOVSKY, M., and J. MCININCH, 1993 GeneMark: parallel gene recognition for both DNA strands. Comput. Chem. 17: 123–133.
BUDIMAN, M. A., L. MAO, T. C. WOOD and R. A. WING, 2000 A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res. 10: 129–136.
BURGE, C., and S. KARLIN, 1997 Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78–94.[CrossRef][Medline]
CHAW, S., A. ZHARKIKH, H. SUNG, T. LAU and W. LI, 1997 Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 14: 56–68.[Abstract]
CHENG, Z. J., and M. MURATA, 2003 A centromeric tandem repeat family originating from a part of Ty3/gypsy-retroelement in wheat and its relatives. Genetics 164: 665–672.
CHENG, Z. K., F. G. DONG, T. LANGDON, O. Y. SHU, C. R. BUELL et al., 2002 Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14: 1691–1704.
COPENHAVER, G. P., K. NICKEL, T. KUROMORI, M.-I. BENITO, S. KAUL et al., 1999 Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468–2474.
DEAN, C., and R. SCHMIDT, 1995 Plant genomes—a current molecular description. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46: 395–418.[CrossRef]
DE JONG, J. H., 1998 High resolution FISH reveals the molecular and chromosomal organization of repetitive sequences in tomato. Cytogenet. Cell Genet. 81: 104.
DOGANLAR, S., A. FRARY, M. C. DAUNAY, R. N. LESTER and S. D. TANKSLEY, 2002 Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161: 1713–1726.
FEINBERG, A. P., and B. VOGELSTEIN, 1983 A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132: 6–13.[CrossRef][Medline]
FOJTOVA, M., A. KOVARIK and R. MATYASEK, 2001 Cytosine methylation of plastid genome in higher plants. Fact or artifact? Plant Sci. 160: 585–593.
FRANSZ, P., W. SOPPE and I. SCHUBERT, 2003 Heterochromatin in interphase nuclei of Arabidopsis thaliana. Chromosome Res. 11: 227–240.[CrossRef][Medline]
FULTON, T. M., R. VAN DER HOEVEN, N. T. EANNETTA and S. D. TANKSLEY, 2002 Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457–1467.
GANAL, M. W., N. L. V. LAPITAN and S. D. TANKSLEY, 1988 A molecular and cytogenetic survey of major repeated DNA-sequences in tomato (Lycopersicon esculentum). Mol. Gen. Genet. 213: 262–268.[CrossRef]
GOFF, S. A., D. RICKE, T. H. LAN, G. PRESTING, R. L. WANG et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.
GOTTSCHALK, W., 1954 Die chromosomenstruktur der Solanaceen unter Berucksichtigung phylogenetischer Fragestellungen. Chromosoma 6: 539–626.[Medline]
HALL, I. M., G. D. SHANKARANARAYANA, K. I. NOMA, N. AYOUB, A. COHEN et al., 2002 Establishment and maintenance of a heterochromatin domain. Science 297: 2232–2237.
INTERNATIONAL RICE GENOME SEQUENCING PROJECT, 2005 The map-based sequence of the rice genome. Nature 436: 793–800.[CrossRef][Medline]
JIANG, J., B. GILL, G. WANG, P. RONALD and D. WARD, 1995 Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc. Natl. Acad. Sci. USA 92: 4487–4491.
JIANG, N., Z. BAO, S. TEMNYKH, Z. CHENG, J. JIANG et al., 2002 Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161: 1293–1305.
JIANG, J. M., J. A. BIRCHLER, W. A. PARROTT and R. K. DAWE, 2003 A molecular view of plant centromeres. Trends Plant Sci. 8: 570–575.[CrossRef][Medline]
JIAO, Y., P. JIA, X. WANG, N. SU, S. YU et al., 2005 A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17: 1641–1657.
JURKA, J., 2000 Repbase update—a database and an electronic journal of repetitive elements. Trends Genet. 16: 418–420.[CrossRef][Medline]
KALENDAR, R., C. M. VICIENT, O. PELEG, K. ANAMTHAWAT-JONSSON, A. BOLSHOY et al., 2004 Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166: 1437–1450.
KOORNNEEF, M., P. FRANSZ and H. DE JONG, 2003 Cytogenetic tools for Arabidopsis thaliana. Chromosome Res. 11: 183–194.[CrossRef][Medline]
KULIKOVA, O., G. GUALTIERI, R. GEURTS, D.-J. KIM, D. COOK et al., 2001 Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J. 27: 49–58.[CrossRef][Medline]
KUMEKAWA, N., T. HOSOUCHI, H. TSURUOKA and H. KOTANI, 2001 The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4. DNA Res. 8: 285–290.[Abstract]
LI, W. L., P. ZHANG, J. P. FELLERS, B. FRIEBE and B. S. GILL, 2004 Sequence composition, organization, and evolution of the core Triticeae genome. Plant J. 40: 500–511.[CrossRef][Medline]
LIPPMAN, Z., A. V. GENDREL, M. BLACK, M. W. VAUGHN, N. DEDHIA et al., 2004 Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471–476.[CrossRef][Medline]
MA, J., and J. L. BENNETZEN, 2004 Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101: 12404–12410.
MAO, L., D. BEGUM, S. A. GOFF and R. A. WING, 2001 Sequence and analysis of the tomato JOINTLESS locus. Plant Physiol. 126: 1331–1340.
MARIN, I., and C. LLORENS, 2000 Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol. Biol. Evol. 17: 1040–1049.
MARTIENSSEN, R. A., P. D. RABINOWICZ, A. O'SHAUGHNESSY and W. R. MCCOMBIE, 2004 Sequencing the maize genome. Curr. Opin. Plant Biol. 7: 102–107.[CrossRef][Medline]
MARTIN, G. B., S. H. BROMMONSCHENKEL, J. CHUNWONGSE, A. FRARY, M. W. GANAL et al., 1993 Map-based cloning of a protein-kinase gene conferring disease resistance in tomato. Science 262: 1432–1436.
MESSEGUER, R., M. W. GANAL, J. C. STEFFENS and S. D. TANKSLEY, 1991 Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear-DNA. Plant Mol. Biol. 16: 753–770.[CrossRef][Medline]
MILLER, J. C., and S. D. TANKSLEY, 1990 Effect of different restriction enzymes, probe source, and probe length on detecting restriction-fragment-length-polymorphism in tomato. Theor. Appl. Genet. 80: 385–389.[CrossRef]
MROCZEK, R. J., and R. K. DAWE, 2003 Distribution of retroelements in centromeres and neocentromeres of maize. Genetics 165: 809–819.
MYSTER, S. H., F. WANG, R. CAVALLO, W. CHRISTIAN, S. BHOTIKA et al., 2004 Genetic and bioinformatic analysis of 41C and the 2R heterochromatin of Drosophila melanogaster: a window on the heterochromatin–euchromatin junction. Genetics 166: 807–822.
NAGAKI, K., Z. CHENG, S. OUYANG, P. B. TALBERT, M. KIM et al., 2004 Sequencing of a rice centromere uncovers active genes. Nat. Genet. 36: 138–145.[CrossRef][Medline]
NESBITT, T. C., and S. D. TANKSLEY, 2002 Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162: 365–379.
OUYANG, S., and C. R. BUELL, 2004 The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32: D360–D363.
PALMER, L. E., P. D. RABINOWICZ, A. L. O'SHAUGHNESSY, V. S. BALIJA, L. U. NASCIMENTO et al., 2003 Maize genome sequencing by methylation filtrations. Science 302: 2115–2117.
PARAN, I., J. R. VAN DER VOORT, V. LEFEBVRE, M. JAHN, L. LANDRY et al., 2004 An integrated genetic linkage map of pepper (Capsicum spp.). Mol. Breed. 13: 251–261.[CrossRef]
PETERSON, D. G., W. R. PEARSON and S. M. STACK, 1998 Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation. Genome 41: 346–356.[CrossRef]
RABINOWICZ, P. D., R. CITEK, M. A. BUDIMAN, A. NUNBERG, J. A. BEDELL et al., 2005 Differential methylation of genes and repeats in land plants. Genome Res. 15: 1431–1440.
RENAULD, H., and S. M. GASSER, 1997 Heterochromatin: A meiotic matchmaker? Trends Cell Biol. 7: 201–205.
RICK, C. M., 1971 Some cytogenetic features of the genome in diploid plant species. Stadler Genet. Symp. 1: 153–174.
SALAMOV, A. A., and V. V. SOLOVYEV, 2000 Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516–522.
SALZBERG, S., A. DELCHER, S. KASIF and O. WHITE, 1998 Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26: 544–548.
SANMIGUEL, P., B. S. GAUT, A. TIKHONOV, Y. NAKAJIMA and J. L. BENNETZEN, 1998 The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43–45.[CrossRef][Medline]
SPOONER, D. M., I. E. PERALTA and S. KNAPP, 2005 Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [Solanum L. section Lycopersicon (Mill.) Wettst.] Taxon 54: 43–61.
SU, P. Y., and T. A. BROWN, 1997 Ty3/gypsy-like retrotransposon sequences in tomato. Plasmid 38: 148–157.[CrossRef][Medline]
SUN, F. L., K. HAYNES, C. L. SIMPSON, S. D. LEE, L. COLLINS et al., 2004 Cis-acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol. Cell. Biol. 24: 8210–8220.
TANKSLEY, S. D., M. W. GANAL, J. P. PRINCE, M. C. DEVICENTE, M. W. BONIERBALE et al., 1992 High-density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160.[Abstract]
VAN DER HOEVEN, R., C. RONNING, J. GIOVANNONI, G. MARTIN and S. TANKSLEY, 2002 Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441–1456.
VOLPE, T. A., C. KIDNER, I. M. HALL, G. TENG, S. I. S. GREWAL et al., 2002 Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833–1837.
WIKSTROM, N., V. SAVOLAINEN and M. W. CHASE, 2001 Evolution of the angiosperms: calibrating the family tree. Proc. R. Soc. Lond. Ser. B Biol. Sci. 268: 2211–2220.[Medline]
WU, J. Z., H. YAMAGATA, M. HAYASHI-TSUGANE, S. HIJISHITA, M. FUJISAWA et al., 2004 Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16: 967–976.
YANG, T. J., S. LEE, S. B. CHANG, Y. YU, H. JONG et al., 2005 In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons. Chromosoma 114: 103–117.[CrossRef][Medline]
YU, J., S. N. HU, J. WANG, G. K. S. WONG, S. G. LI et al., 2002 A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79–92.
ZHONG, C. X., J. B. MARSHALL, C. TOPP, R. MROCZEK, A. KATO et al., 2002 Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14: 2825–2836.
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