Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S

Abstract

SummaryTelomeres, which are important for chromosome maintenance, are composed of long, repetitive DNA sequences associated with a variety of telomere-binding proteins. We characterized the organization and structure of rice telomeres and adjacent subtelomere regions on the basis of cytogenetic and sequence analyses. The length of the rice telomeres ranged from 5.1 to 10.8 kb, as revealed by both fibre-fluorescent in situ hybridization and terminal restriction-fragment assay. Physical maps of the chromosomal ends were constructed from a fosmid library. This facilitated sequencing of the telomere regions of chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. The resulting sequences contained conserved TTTAGGG telomere repeats, which indicates that the physical maps partly covered the telomere regions of the respective chromosome arms. These repeats were organized in the order of 5¢-TTTAGGG-3¢ from the chromosome-specific region, except in chromosome 7S, in which seven inverted copies also existed in tandem array. Analysis of the telomereflanking regions revealed the occurrence of deletions, insertions, or chromosome-specific substitutions of single nucleotides within the repeat sequences at the junction between the telomere and subtelomere. The sequences of the 500-kb regions of the seven chromosome ends were analysed in detail. A total of 598 genes were predicted in the telomeric regions. In addition, repetitive sequences derived from various kinds of retrotransposon were identified. No significant evidence for segmental duplication could be detected within or among the subtelomere regions. These results indicate that the rice chromosome ends are heterogeneous in both sequence and characterization.

Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

“…The telomeres of 31 rice accessions (both cultivars and wild species, which belong to AA, BB, BBCC, CC, CCDD, GG, or HHJJ species of Oryza) are 5 to 20 kb in length [24]. Marked variation in telomere length is also observed among cultivated rice of the AA genome: the japonica cultivar Nipponbare shows a relatively low MW pattern and the indica cultivar Kasalath shows a relatively high MW pattern.…”

“…These telomeric repeats are organized in the order of 5′-TTTAGGG-3′ from the chromosome-specific region [24,42]. The sevennucleotide unit has deletions, insertions, or substitutions of single nucleotides near the junction between the telomere and the chromosome-specific region.…”

“…As the restriction enzymes used in the construction of PAC/BAC libraries could not cut the canonical telomere array, (TTTAGGG)n, the libraries did not contain the clones derived from telomeric sequences [5,39]. To capture the telomere sequences, a rice fosmid library constructed by the cloning of random mechanically sheared DNA [1] was screened [24]. The library enabled telomeric sequences to be obtained without the constraints imposed by enzyme site preferences.…”

MEIOTIC F-BOX Is Essential for Male Meiotic DNA Double-Strand Break Repair in Rice

“…To investigate telomere bouquet formation in the wild type and mof, we conducted fluorescent in situ hybridization (FISH) analysis using Cy3-probe labeled telomere-specific sequences as described (Mizuno et al, 2006). In wild-type rice male meiocytes, telomeres attached to the nuclear envelope and clustered together at early prophase I, showing a typical bouquet configuration ( Figure 3A).…”

“…The FISH procedure was performed as described (Cheng, 2013). The sequence of the telomere FISH probe is (TTTAGGG) 7 labeled with Cy3 as described (Mizuno et al, 2006). BAC clone P0671B11 was kindly provided by B. Han (National Center for Gene Research, Shanghai, Institutes for Biological Sciences, Chinese Academy of Sciences).…”