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. 2006 May;173(1):401-17.
doi: 10.1534/genetics.105.055202. Epub 2006 Mar 17.

Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end

Hui-Fen Kuo  1 , Kenneth M Olsen, Eric J Richards
Affiliations

Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end

Hui-Fen Kuo et al. Genetics. 2006 May.

Abstract

We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (approximately 3.5 kb), which represents the relatively simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4-kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4-kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated nonhomologous end-joining (NHEJ) events. There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome-healing events associated with terminal deletions of the subtelomeric region as well as the capture of a scrambled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini.

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Figures

Figure 1.
Figure 1.
Genomic organization of chromosome 1N subtelomeric region from A. thaliana accession Columbia. The terminal telomeric repeat array is depicted as a thick solid arrow oriented toward the end of the chromosome. The most distal gene, At1g01010, is shown as an open rectangle with an arrow indicating the direction of transcription. Vertical numbers marked above the chromosome are coordinates in the most current version of the Col genomic sequence (TAIR 6.0) and denote the boundaries of the subtelomeric region defined in this study. Various sequence features are shown below the chromosome map. The position and orientation of primers used in this study are shown by arrowheads below; primer names correspond to nucleotide coordinates.
Figure 2.
Figure 2.
Summary of polymorphic sites over the 1442-bp telomere-proximal region of chromosome 1N among 35 accessions. A map of chromosome 1N subtelomeric region from accession Columbia is shown on the top (as in Figure 1). At the bottom, an expanded 1442-bp region is diagrammed. Vertical bars represent single nucleotide substitutions; vertical bars with triangules indicate insertions (∇) and deletions (Δ) of ≤11 bp. Open boxes below the lines indicate larger-scale deletions (>30 bp) and the striped box denotes a deletion (409 bp), which is replaced by a copia-like LTR sequence (470 bp); accessions carrying these alterations are labeled. Asterisks mark the sites where a sequence inversion occurred (vertical numbers indicate the nucleotide coordinates of the breakpoints) along with deletions of the flanking sequences (stippled boxes); this complex rearrangement is observed in accessions Bur-0, Ct-1, Cvi-0, Oy-0, and Ws-2. Singleton sites are polymorphisms found in only one accession, whereas nonsingleton sites are found in more than one accession. The dashed regions along the chromosomal lines are sequence gaps at the poly G tract (the shaded region on the map at the top).
Figure 3.
Figure 3.
Five classes of subtelomeric structures at chromosome 1N among 35 accessions. (A) Diagrams depict the large-scale DNA rearrangements that define five classes of subtelomeric structures at chromosome 1N. Telomeric repeats are shown as solid boxes; the chromosome end is oriented toward the right. The accessions in each class are shown at the right. Intersecting dashed lines indicate the large 1432-bp inversion and deletions are shown as gaps. The striped box denotes a copia-class LTR insertion; putative 5-bp _target site duplication (TSD) sequences flanking the LTR termini signature (5′-tg … ca-3′) are indicated. (B) Sequence alignment of Col and class 4 accessions showing two subterminal deletion breakpoints; nucleotide coordinates correspond to the Col genomic sequence (TAIR 6.0). Dots are conserved nucleotides; upper case letters denote discontinued sequence alignments, with canonical repeats (TTTAGGG) highlighted in boldface type and italics; dashed lines with arrowheads point to the chromosome end. TT dinucleotides at the novel subtelomeric–telomeric sequence junction are underlined.
Figure 4.
Figure 4.
Phylogenetic relationship among chromosome 1N subtelomeric and telomeric haplotypes. (A) A tree containing 19 A. thaliana haplotypes and 1 A. suecica haplotype was constructed on the basis of maximum parsimony criterion and a data set covering the 1442-bp distal subtelomeric region. Each mutation step (including single nucleotide substitutions and indels <11 bp) is represented by a line segment and nodes represent unknown/missing haplotypes. Shaded areas highlight accessions with class 2 and class 4 subtelomeric structures. The dashed lines enclose accessions/haplotypes with a mitochondrial DNA (mtDNA) sequence captured in the telomeric array. The thick shaded line distinguishes two clusters of subtelomeric haplotypes that represent two major length morphs of the DV regions DV ∼85 bp and DV ∼221 bp as indicated (not including Kas-2, Tamm-27, Shakdara, and Kz-1). (B) A consensus parsimony tree (>50% majority) based on the DV region (positions 1–276 in Figure 5). Four A. thaliana accessions (Kas-2, Tamm-27, Shakdara, and Kz-1) were not included because of large deletions over the aligned region. The tree is generated by a heuristic search, excluding the gap features at position 222 and 231 in Figure 5 due to ambiguous alignments. Col** haplotype includes 11 accessions: Br-0, Col, Knox-10, Knox-18, Ler-1, Ms-0, Ra-0, Wa-0, Wei-0, Ws-0, and Ts-1. The numbers along the branches indicate percentage of total trees showing the topology indicated by the flanking nodes.
Figure 5.
Figure 5.
Alignment of the centromere-proximal telomeric region of chromosome 1N from 35 A. thaliana accessions and 9 accessions of A. suecica. Accessions are indicated on the left of the corresponding nucleotide sequences, which are shown in two tiers, oriented 5′ to 3′ toward the end of the chromosome. Vertical numbers on the top indicate the nucleotide positions within the telomeric repeat sequences distal to the subtelomeric sequence. Canonical telomeric sequence (TTTAGGG) is highlighted in blue; nucleotide polymorphisms are shown in red, as is the position of the 104-bp mtDNA sequence. Dashes denote alignment gaps. Arrowheads in gold indicate examples of indels of adjacent direct repeats. The haplotype represented by Col/Ler-1* also includes accessions: Knox-10, Knox-18, Ms-0, Wa-1, Wei-0, and Ws-0. The A. suecica** haplotype includes all 9 accessions of this species sampled in this study.
Figure 6.
Figure 6.
Sequence alignment of the DV region and 104-bp nontelomeric sequence in the Chr1N telomere among 12 accessions. (A) The mitochondrial genomic sequences that are identical to the 104-bp sequence in the telomeric array are highlighted in blue and gold, and the flanking genomic sequences are in lowercase letters. Nucleotides with identity at the junction of the breakpoints are underlined. The canonical telomeric repeats are shown in blue, dots denote nucleotides that match the reference sequence corresponding to accession Col, and alignment gaps are indicated by red dashes. (B) A map of the A. thaliana mitochondrial genome (based on sequence from the C24 accession) showing the positions and orientations of the two mtDNA segments that compose the 104-bp sequence captured in the telomeric repeat array. (C) An expansion of a tip of the phylogenetic tree shown in Figure 4A, based on incorporation of polymorphisms within the centromere-proximal domain of the telomeric repeat array shown in A. Layout is the same as that described for Figure 4A, except that polymorphisms within the telomeric region (indels of telomeric repeats and one single nucleotide substitution) are marked by dashed lines to distinguish them from subtelomeric polymorphisms (solid lines).
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