Toward closing rice telomere gaps: Mapping and sequence characterization of rice subtelomere regions

Tae Jin Yang, Yeisoo Yu, Song Bin Chang, Hans De Jong, Chang Sik Oh, Sang Nag Ahn, Eric Fang, Rod A Wing

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Despite the collective efforts of the international community to sequence the complete rice genome, telomeric regions of most chromosome arms remain uncharacterized. In this report we present sequence data from subtelomere regions obtained by analyzing telomeric clones from two 8.8 x genome equivalent 10-kb libraries derived from partial restriction digestion with HaeIII or Sau3AI (OSJNPb HaeIII and OSJNPc Sau3AI). Seven telomere clones were identified and contain 25-100 copies of the telomere repeat (CCCTAAA)n on one end and unique sequences on the opposite end. Polymorphic sequence-tagged site markers from five clones and one additional PCR product were genetically mapped on the ends of chromosome arms 2S, 5L, 10S, 10L, 7L, and 7S. We found distinct chromosome-specific telomere-associated tandem repeats (TATR) on chromosome 7 (TATR7) and on the short arm of chromosome 10 (TATR10s) that showed no significant homology to any International Rice Genome Sequencing Project (IRGSP) genomic sequence. The TATR7, a degenerate tandem repeat which is interrupted by transposable elements, appeared on both ends of chromosome 7. The TATR10s was found to contain an inverted array of three tandem repeats displaying an interesting secondary folding pattern that resembles a telomere loop (t-loop) and which may be involved in a protective function against chromosomal end degradation.

Original languageEnglish (US)
Pages (from-to)467-478
Number of pages12
JournalTheoretical And Applied Genetics
Volume111
Issue number3
DOIs
StatePublished - Aug 2005

Fingerprint

telomeres
Telomere
Tandem Repeat Sequences
chromosomes
rice
Chromosomes, Human, Pair 7
tandem repeat sequences
Clone Cells
Chromosomes
Genome
Sequence Tagged Sites
clones
Chromosomes, Human, Pair 10
DNA Transposable Elements
genome
Libraries
Digestion
transposons
Polymerase Chain Reaction
Oryza

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Horticulture
  • Plant Science
  • Genetics
  • Genetics(clinical)

Cite this

Toward closing rice telomere gaps : Mapping and sequence characterization of rice subtelomere regions. / Yang, Tae Jin; Yu, Yeisoo; Chang, Song Bin; De Jong, Hans; Oh, Chang Sik; Ahn, Sang Nag; Fang, Eric; Wing, Rod A.

In: Theoretical And Applied Genetics, Vol. 111, No. 3, 08.2005, p. 467-478.

Research output: Contribution to journalArticle

Yang, Tae Jin ; Yu, Yeisoo ; Chang, Song Bin ; De Jong, Hans ; Oh, Chang Sik ; Ahn, Sang Nag ; Fang, Eric ; Wing, Rod A. / Toward closing rice telomere gaps : Mapping and sequence characterization of rice subtelomere regions. In: Theoretical And Applied Genetics. 2005 ; Vol. 111, No. 3. pp. 467-478.
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