DNA RESEARCH 6, 381-386 (1999) Structural Analysis and Complete Physical Map of Arabidopsis thaliana Chromosome 5 Including Centromeric and Telomeric Regions Hirokazu KOTANI,* Tsutomu HOSOUCHI, and Hisano TSURUOKA Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292, Japan (Received 1 December 1999) Abstract Previously, we have reported a fine physical map of Arabidopsis thaliana chromosome 5, except for the centromeric and telomeric regions, by ordering clones from YAC, PI, TAC, and BAC libraries of the genome consisting of the two contigs of upper arm and lower arm, 11.6 M bases and 14.2 M bases, respectively.1 Here, the remaining centromeric and telomeric regions of chromosome 5 are completely characterized by the ordering of clones and PCR amplifications. Chromosome 5 of Arabidopsis thaliana ecotype Columbia is about 28.4 M bases long. The centromeric region is estimated at about 2 M bases long between two 5S-rDNA clusters. The 180-bp repeat region mainly consists of blocks of 180-bp tandem family and various type retroelements dispersed over a 500-kb region. The telomeric regions of chromosome 5 are characterized by PCR cloning, sequencing and hybridization. The telomere repeats at both ends are about 2.5-kb long and interestingly, telomere-associated repeats (~700 bp) are found near both ends of chromosome 5. Key words: Arabidopsis thaliana chromosome 5; physical map; contig map; telomere; centromere presence of repetitive sequences are, nevertheless, known to be involved in processes essential for cellular functions Because of the relative ease of genetic manipula- such as meiosis, mitosis, chromosomal stability and nutions, its short life cycle, and other unique character- cleolar organization. The key to a full understanding of istics, Arabidopsis thaliana is now considered to be a these functions is, of course, elucidation of the fine strucmodel organism for the study of various aspects of bi- ture of these regions at the nucleotide level. At present, it ological phenomena associated with higher plants. Ef- is known that the A. thaliana centromeres are heterochroforts to sequence the entire genome (approximately matic, contain tandem arrays of 180-bp repeats cover130 Mb) of the plant, initiated in 1996 by an inter- ing approximately 1 M bp, and resemble those of human national consortium, have so far yielded sequence data chromosomes in size and genomic organization.5 The role for approximately 70% of the genome (http://genome- of the telomeric repeats of A. thaliana (5'-TTTAGGGwww.stanford.edu/Arabidopsis/agi.html) and are ex- 3') is still not well understood but it seems highly likely pected to be completed by the end of the year 2000, ex- that these repeats are involved in cellular senescence.6 cept for highly and moderately repetitive DNA regions Following previous work,1 we constructed a complete including telomeres, centromeres and nucleolar organi- physical map by the ordering of YAC and BAC clones zation regions (NOR). Along the efforts, physical maps for the centromere region and PCR amplifications for the of A. thaliana chromosomes have been constructed by telomeric regions of A. thaliana chromosome 5. the ordering of PI, TAC, BAC, and YAC clones except for telomeres, centromeres and NORs. 14 The regions (telomeres, centromeres and NORs) left out from the ini- 2. Materials and Methods tial efforts to sequence the entire genome because of the 2.1. Libraries, screening, clone analysis and sequencing To construct a physical map of the centromeric region Communicated by Michio Oishi * To whom correspondence should be addressed. Tel. +81-438- by clone ordering, PCR screening of DNA pools was done 52-3920, Fax. +81-438-52-3921, E-mail: [email protected] to identify positive clones harbored in YAC, IGF BAC, t The nucleotide sequence data of the upper telomere and the 1 lower telomere regions will appear in the DDBJ, EMBL and and TAMU BAC libraries as described previously. SeGenBank nucleotide sequence databases with accession num- quencing of TAMU4G15.2 and the telomere regions was bers AB033277 and AB033278, respectively. done by the shotgun and/or primer walking method us1. Introduction [Vol. 6, Complete Physical Map of Arabidopsis thaliana Chromosome 5 388 CO O a a. -11.1 Mb 0.2 Mb •+• 3.9 M b — - I - i Upper telomere '"-'•:'.:• SS-rDNA Repeats Cltj(ME04, <2Stft(B \ 'o.i Mb . . • • • . " • • • . ' - . • • . " • • ' ' . : ? ; • • •• • • • • . " • • ' ' • '••' L o w Centromere region CICO7A02. 460KB 13.3 Mb i e Total 28.6 Mb r lelomere - - -. 5S-fDNA Repeats 180-bp Repeats region I CIC04F1O,36OKB I | CIC06A01. 4 5 0 K B ~ l I CtC11fQ1.5Z0KS CIC03D06, a30KB~ [CtC1Z003,360KB| Q : 26J33 M IGF12KI9 •MTAM20K19 |TAfc0003 I IMCJ3 ' Centromere Region 2 Mb TAMU4G15_2 18OUP Repeats 10 kb Figure 1. Genomic organization of A thaliana chromosome 5. a. Schematic structure of A. thaliana chromosome 5. A fine physical map from PDC3 to nga76 and PhyC to CD3-42 was described previously.1 The centromere region, 5S-rDNA cluster locus and telomere repeats are indicated by red, yellow and blue bars, respectively, b. A physical map of the A. thaliana chromosome 5 centromere region. The name and size of the CIC YAC clones are indicated in wide-open boxes. Bacterial clones constituting the minimum tiling path are shown by open boxes (previous work1) and closed boxes (this work) below the wide YAC boxes. The names of bacterial clones are indicated on the right side of the boxes as PI ( M # # # ) , TAC ( K # # # ) , IGF BAC ( I G F # # # ) and TAMU BAC ( T A M # # # ) . The red and the light blue striped box show the 180-bp repeat region and 5S-rDNA cluster locus, respectively, c. Schematic structure of the TAM4G15.2 clone. The red striped boxes show the block of 180-bp repeats. The black and gray boxes show the regions homologous to LTR and inner sequence of the Athila retroelement, respectively. The green and the striped boxes show high homology regions to the LTR-like and inner sequences of the retro-like element coded in T9E19, respectively. The yellow and purple boxes show low homology regions to the LTR-like sequence of the retro-like element coded in T9E19. ing a Big dye terminator cycle sequencing kit, and the 3. Results and Discussion sequences were assembled by an Autoassembler (PerkinConstruction of physical map of centromeric region Elmer-ABI, Foster, CA). Sequence data were subjected 3.1. For construction of the physical map of the cento homology search by the BLAST and FASTA programs tromeric regions, we isolated 4 YAC clones and 230 (GCG, Madison, WI). BAC clones by PCR screening from BAC end sequences and ordered them. The order was confirmed 2.2. Characterization of telomere regions PCR using primers designed from end sequences as by For the amplification of telomeric regions, LA well as the information obtained from restriction entaq (TAKARA, Kyoto, Japan) and the following zyme digestion patterns of the isolated clones compared primers were used: A. thaliana telomere primer in the BAC fingerprint data base (http:// to those (5'-CCCTAAACCCTAAACCCTAAACCCTAAACC-3'), and IGF genome.wustl.edu/gsc/arab/arabidopsis.html) IGF10P11SP primer (5'-TTTCTCGGCTTTCCTCTGBAC Contig data base (http://194.94.225.l/private_ ACATGGCATCTC-3'), K9I9T7 primer (5'-AACTAGCTTCATATGGGGAAGACGATGCTC-3'), and yeast workgroups/pg_101/bac.html). A complete physical map telomere primer (5'-CACACCCACACACCACACCCA- of the chromosome 5 centromeric region of A. thaliana CAC-3')- The LA PCR mixture was held at 96° C for was thus constructed as shown in Fig. 1. Recently, Tutois 3 min, subjected to 35 cycles at 96°C for 30 sec and et al. reported the partial contig mapping of the pericen-7 68°C for 10 min and then held at 4°C. [[Aren't there 3 tromeric region of chromosome 5 using a YAC library. stages to the PCR cycle? Denaturation, annealing, and However, the orientation of their map differs from that of ours. Their orientation might be based on the interextension?!] H. Kotani, T. Hosouchi, and H. Tsuruoka No. 6] YpAt7(A thaliana Landsberg) Telomere repeats AB033277 -2.5 kb III) 1)1) IGF10P11 TAS -2.5 kb Telomere repeats AB033278 T9I9 CIC3B1L, 670 kb > Yeast Telomere Telomere repeats 1 kb Figure 2. Schematic structures of the upper and lower telomere regions of A. thaliana chromosome 5. a. Structure of the upper telomere region, b. Structure of the lower telomere region. The blue and yellow boxes show telomere repeats and variant telomere repeats, respectively. The red arrows and light blue striped boxes indicate TAS and homologues regions between the upper telomere region and YpAt7, respectively. The solid bars show the sequenced regions, and accession numbers are indicated on the right side of the solid bars. The green boxes show the end positions of the IGFlOPll and T9I9 clones. The purple box shows the schematic structure of CIC3B1L. D, HD, and HP below the solid bars are Dra I, Hindlll, and Hpa I restriction sites, respectively. The red bar shows the probe for the Southern hybridization used in Fig. 4. pretation of hybridization and the chimera YAC clone, CIC9F5, as the upper anchor clone. A. thaliana pericentric heterochromatin can be subdivided into a central domain, the functional centromere, and two flanking domains as revealed by FISH experiments using pachytene chromosomes. In A. thaliana (Columbia ecotype) chromosome, 5S-rDNA loci have been mapped to the pericentromeric heterochromatin regions of chromosome 3, the short arm of chromosome 4 and the upper arm of chromosome 5.8 We found, however, that two loci of 5SrDNA clusters are located between the nga76 and PhyC markers. The first 5S-rDNA gene cluster is located at a site approximately 500 kb distal to nga76. The cluster should consist of over 200 copies of the 5S-rDNA gene as evidenced from the fact that (1) clone CIC4E4 (< 250 kb) covered this 5S rDNA cluster completely and (2) approximately one-half of the region in this YAC clone, which was covered by clone TAMU30A15, did not contain a 5S rDNA gene cluster. The second 5S rDNA cluster covered by clone TAM19B10 is located at a site approximately 2 Mb from the first and consists of approximately 30 copies of the 5S rDNA gene as determined by Southern hybridization and partial sequencing. In the fluorescence in situ hybridization (FISH) picture of chromosome 5 in Murata et al.,8 the satellite signal 5S-rDNA was observed at the top end of the lower arm of chromosome 5. Also, Fransz et al. reported that a minor 5S-rDNA locus in the lower arm of chromosome 5 was often detected in several ecotypes of A. thaliana including Columbia.9 The satellite signal was probably the second 5S-rDNA cluster on our physical map. In the central domain, the 180-bp tandem repeats and the 106B family10 are interspersed rather than forming separate regions in the five Arabidopsis chromosomes.9 This 180-bp tandem repeated DNA sequence is present in arrays of over 50 kb, has been shown to locate in the heterochromatin moiety surrounding the centromere11'12 and to hybridize equally to both sides of the centromere on all five chromosome pairs.13 Among the two 5S-rDNA clusters, the blocks of 180-bp tandem repeats were dispersed over approximately 500 kb as confirmed by PCR, restriction patterns and partial sequencing of the subclones derived from clones comprising this region. One clone, TAMU4G15_2 (approximately 75 kb, the sequence Complete Physical Map of Arabidopsis thaliana Chromosome 5 384 Lower TAS(C) Upper TAS(C) YpAt7 TAS 3069 ACCATATACCTATACCATACCCTAAATCOCTATACCATATACCCTATACCCT 1 TATACCATGTACCCTCAACCTTAAAACCCT ATAACCCTAAACCCCTATACCCTAAAACCCTATACCATGTACCCTCAACCTTAAATCCCT Lower TAS(C) Upper TAS(C) YpAt7 TAS ATACCCTATACCCTAAATCCCTAAACCCTAAACTCTAAACC3TAGGGTTTATGAGTTTGC AAAACCTATACTATAAATCTTTAAAACCTATACTCTAAACCVTAGGGTTTGTGAGTTTGC AAAACCTATACTATAAATCTTTAAAACCTATACTCTAAACC VTAGGGTTTGTGAGTTTGC Lower TAS(C) Upper TAS(C) YpAt7 TAS ATAAAGTGTCTTGTATAAGTGTTTCTAACATGTGAGTTTGCATAAGAGTC-TCAACTATG ATAAAGCGTCACGTATAAGTGTTTCTAACATGTGAGTTTGCATAAGAGTC-TCGACTATG ATAAAGTGTCACGTATAAGTGTTTCTAACATGTGAGTTTGCATAAGAGTCCACGTATAAG Lower TAS(C) Upper TAS(C) YpAt7 TAS TGTTTGTTCAAACGTGACGTAAGTGTTTAGACCAGAGCCGGCCGTGAGCACAAGCGGGTC TGTTTGTTCAAAAGTGACGTAAGTGTTTAGACTAGAGCCGGCCGTGAGCACAAGCGGGCC TGTTT -CTAACATGTGA GTTT- -GC ATAAG AGTCCCGTGAGCACAAGC-GGCC Lower TAS(C) Upper TAS(C) YpAt7 TAS AAGCCCATGCTTGCGGCCGATTATCATATAATTATGTTTTGCTGCTTCATAATTTTGAAA AAGCCCATGCTTGCGGCAGATTATCCTATAATTATGTTTTGCGGCTTTACAATTTTGAAT AAGCCCATGCTTGCGGCAGATTATCCTATAATTATGTTTTGCGGCTTCACAATTTTGAAA Lower TAS(C) Upper TAS(C) YpAt7 TAS TTGTTTTGTGGTTAAGTGGTCGGGTCGGAGATGAGTTAGTTCTCATAC ATCTC AAA - TTC TTGTTTTGTTGTTTAGTGGTCGAGTCAGGGATGAGTTTGTTCTCAAACATCTCAAATTTC TTGTTTTGTTGTTTAGTGGTCGAGTCAGGGATGAGTTTGTTCTCAAACATCTCAAATTTC Lower TAS(C) Upper TAS(C) YpAt7 TAS AAATCTTCCAAAATGTTAGGTTCACTCTACTTTATTTTATTTTTATTTTTTA-AGTTTAA TAATCTTCC-AAGTGTTAGGTTCACTCTACCTTATTTTTTTTTTTTTTTTTT-ATTTTAA TAATCTTCC-AAGTGTTAGGTTCACTCTACCTTATTTTTTTTTATTTTTTTTTATTTTAA Lower TAS(C) Upper TAS(C) YpAt7 TAS ATTTCCATTAGAAATAACTTGAACTTTATTTCAAATGAACATTAGAAAGAATTGTCACTC ATTTCTATTAGAAAGAACTTGAACCTTATTTCAAGTGAACATTAAAAAGAATTGTAACCC ATTTCTATTAGAAAGAACTTGAACCTTATTTCAAGTGAACATTAGAAAGAATTGTAACCC Lower TAS(C) Upper TAS(C) YpAt7 TAS TACCTTATTTCTATTATTATGAATACGTGTAAAGTAATTCTTTTTTACAATAAACATGTA TACCTTATTTCTATTATTATGAATATGTGTAAAGTAAAT-TTTTTTACAATAAGCATGTA TACCTTATTTCTATTATTATGAATATGTGTAAAGTAAAT-TTTTTTACAATAAGCATGTA Lower TAS(C) Upper TAS(C) YpAt7 TAS TAAAGTGACCTACTTTTGTTCTTTTCTTATAGCCTTGTAAATCATAGGGACGGCTCTAGT TAAAGTAACATATTTTTGTTCTTTTCTTATAGCCTTGTAAATCATAGGGACGGATCTAGT TAAAGTAACCTATTTTTGTTCTTTTCTTATAGCCTTGTAAATCATAGGGACGGATCTAGT Lower TAS(C) Upper TAS(C) YpAt7 TAS TT AGAATAAAGTGTTGC ATAAGTGCTTCG ACTAAC ATATGAGTCC ATTTTTGTGAG - TTT TTAGAATAAAGTGTTGCATAAGTTCTTCGACTAACATATGAGTCCATTTTTGTGAGTTTT TTAGAATAAAATGTTGCATAAGTGCTTCGACTAACATATGAGTCCATTTTTGTGAGTTTT Lower TAS(C) Upper TAS(C) YpAt7 GCATAAGTGTTGCGCGTTCGACAATTTGAATTTGATGCATAAGTGCTTTGACTAATTTAT GCATAACTTTTGCGCCTTCGACAATTTGAATTTTATGCATAAGTGCTTTGACTAATTTAT GCATAACTTTTGCGCCTTTGACAATTTGAATTTTATGCATAAATGCTTTGACTAATTTAT Lower TAS(C) Upper TAS(C) YpAt7 TAS GAGTTTTGTCTAAGTGATTCGACATTTCGACTAA ATGTTTTGTCTAAGTGATTCGACATTTCGACTAA ATGTTTTGTCTAAGTGATTCGACATTTCGACTAA [Vol. 6, 2328 A. thaliana ecotype Columbia Chromosome 5 720 A. thaliana ecotype Columbia Chromosome 5 A. thaliana ecotype Landsberg Z12170 Figure 3. Alignment of T A S sequences of the upper and lower telomere regions of A. thaliana ecotype Columbia and Y p A t 7 of ecotype Landsberg. The red and green letters show same bases among three T A S s and the direct repeat in TASs, respectively. The variant telomere repeats are boxed. of this clone will appear in the near future.), which mapped to the left side of the 180-bp repeats region was analyzed by sequencing. As shown in Fig. lc, this region consisted of six 180-bp repeats blocks (0.5 ~ 12 kb) and several full or partial sized retro elements containing long terminal repeats (LTR). In A. thaliana, two types of retrotransposons have been described.14'15 The Tal retrotransposon was the first transposable element shown to carry all the structural and coding features characteristic of retrotransposon.14 A second type of retroelement called Athila found in the heterochromatin region has the characteristics of retrotransposons such as LTRs, primer binding site (PBS) and polypurine tract (PPT). In T4G15.2, a LTR like sequcence of Athila LTR (> 90%), two Athila type retro-like elements coded in TAMU9E19 (afl04920.gb.pl2), and two LTR like sequences with low homo logy (> 60% against the LTR of T9E19) are found. Southern hybridization of the ordered clones of the 180-bp repeats region (500 kb) using LTR probe of the retro like element of the T9E19 clone showed that the 180-bp repeats region contained over 20 copies of LTR sequence (data not shown). This means that this region is a mosaic structure of the block of 180-bp repeats and retro-elements like the T4G15.2 clone. Based on the density of the heterochromatin (> 300 kb/nm) and the average size of 180-bp repeats No. 6] H. Kotani, T. Hosouchi, and H. Tsuruoka hybridizing region (1.5-1.8 nm) discussed by Fransz et al.,9 it is estimated that the 180-bp repeat region is more than 450 kb long. This value is consistent with the 180bp region of our map (Fig. lb) and similar to that for the fully functional centromere of Drosophila minichromosome (420 kb).16 Preuss et al. reported a technique that utilizes tetrad analysis to identify the chromosomal domains that contain the functional centromere.17 It is necessary to further research the locus of the functional centromere. 385 1 2 3 ** .23.1 Kb .9.41 Kb -6.55 Kb •4.36 Kb 3.2. Structures of telomeric regions of chromosome 5 Previously,1 we isolated MQA11 as the upper end 1949 bp clone, and K9I9 and CIC3B1L as lower end clones. Further genome walking using the BAC library was then carried out. One clone, IGF10P11, was isolated as a upper end clone by PCR screening using primers of 825 bp MQA11T7 end. Nevertheless, further genome walking 599 bp for both ends using primers of IGF10P11SP end for the upper direction and K9I9T7 end for the lower direction 333 bp did not succeed. It seemed that IGF10P11 and K9I9 were closely linked to the upper and the lower telomere regions, respectively. Therefore, PCR amplification was done to characterize the structure of the telomere- Figure 4. Southern hybridization of the telomere regions of A. thaliana chromosome 5. 2 fig of genomic DNA was digested by associated regions of A. thaliana Columbia chromosome ffindlll (lane 1), Dra I (lane 2) and Hpa I (lane 3). * and ** 5 using primers of telomere repeats and end clones. In show the upper and lower telomere regions containing telomere repeats, respectively. Signals of 1949 and 333 bp are driven by the case of the upper telomere region, an approximately Dra I fragments of the upper telomere region. Signals of 825 4.8 kb of DNA fragment was amplified. Through seand 599 bp are driven by Dra I fragments of the lower telomere quence analysis and a BLAST search, this amplified fragregion. Probe was used for the upper TAS region as shown in ment (Accession No. AB033277) was found to be highly Fig. 2. Arrows show A Hindlll fragment size markers. homologous to the YpAt7 which contained the telomeric region of A. thaliana Landsberg erecta isolated by 17 Richards et al.18 as shown in Fig. 2. So, we concluded upper, lower telomeric regions and YpAt7 shows good that this amplified fragment was the upper telomere of homology including 15-bp direct repeats (Fig. 3). Southern hybridization revealed TASs to be specific for both chromosome 5 and is linked to the IGF10P11 clone. In the case of the lower telomeric region, PCR ampli- ends of chromosome 5 (Fig. 4. Lane 2; the signals of fication from genomic DNA using the telomere primer 1949 bp and 333-bp are from the upper TAS region, and and K9I9T7 primer was not successful. Previously, we the signals of 825 bp and 599 bp are from the lower TAS characterized the CIC3B1 clone as containing two YACs, region) and the telomere repeats of the two regions to termed CIC3B1S and CIC3B1L. CIC3B1L was mapped be approximately 2.5 Kb long (Fig. 4. Lanes 1 and 3). to the lower end of chromosome 5 and covered the K9I9 Adjacent to the terminal telomeric repeat array is a reclone completely.1 Futhermore CIC3B1L was unstable gion that contains a number of more variable repeated and lacked the R arm of pYAC4.19 Because of the possi- sequences, which may be shared by nonhomologous chrobility that CIC3B1L covered the lower telomeric end of mosome ends, and TAS repeats show a polymorphic dischromosome 5, PCR amplification from CIC3B1L DNA tribution with respect to both the position and the20 numwas done using K9I9T7 primer and a yeast telomere bers of repeats found on any one chromosome. The primer. Approximately 4 kb of DNA was amplified. The 700 bp TASs at either end of the same chromosome are sequence (Accession No. AB033278) of this DNA frag- unknown and may be a unique feature of A. thaliana. ment contained 40 telomere repeats (TTTAGGG) of A. chromosome 5. Although the telomeric repeat array is thaliana. Thus, we concluded that CIC3B1L covered essential and sufficient for protecting the integrity and the lower telomeric region of chromosome 5. Interest- stability of the chromosome end, the function of TAS ingly, approximately 700 bp of the telomere associated is not clear. The function of telomeres and/or TAS is sequences (TASs) following the variant telomere repeats speculated to be association with the nuclear membrane, were found at both ends of chromosome 5 as shown in an important role in chromosome movement, association Fig. 2 and the alignment among the TAS sequences of and pairing of chromosomes during meiosis,21'22 the high rate of recombination23 and unequal sister chromatid 386 Complete Physical Map of Arabidopsis thaliana Chromosome 5 exchange.24 Moreover, TASs of chromosome 5 may affect the recognition of both ends of one chromosome. We have here reported the fine structure of the remaining centromeric and telomeric regions, thus completing construction of the physical map of A. thaliana chromosome 5. Based on the results presented here and in a previous study,1 chromosome 5 of A. thaliana is estimated to be approximately 28.4 Mb long and to consist of an 11.7 Mb upper arm (upper telomere to first 5S rDNA locus), 2 Mb centromere region (first 5S-rDNA locus to second 5S-rDNA locus) and 14.9 Mb lower arm (second 5S rDNA locus to lower telomere) (Fig. la). Sequencing of the entire centromeric region by using ordered clones is now in progress and will be completed in the near future. Acknowledgements: We are grateful to Drs. S. Choi and R. Wing of Texas A & M University, T. Altman of the Max Plank Institute and I. Bancroft of the John Innes Centre for providing the TAMU and IGF BAC libraries. We thank Ms. A. Sueda and Ms. E. Usami for their skillful technical assistance and Ms. A. 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