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Type: Journal article
Title: Exact word matches in rice pseudomolecules
Author: Liu, S.
Tinker, N.
Mather, D.
Citation: Genome, 2006; 49(8):1047-1051
Publisher: Natl Research Council Canada
Issue Date: 2006
ISSN: 0831-2796
Statement of
Shaolin Liu, Nicholas A. Tinker, and Diane E. Mather
Abstract: Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) “words” across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes; these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.
Keywords: Oligonucleotide; sequence repetition; word match frequency; rice
RMID: 0020061910
DOI: 10.1139/G06-055
Appears in Collections:Agriculture, Food and Wine publications

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