Feb 10, 2015

Uncovering Long Palindromic Sequences in Rice (Oryza sativa subsp. indica) Genome

BioRxiv : the Preprint Server for Biology
Asadollah AhmadikhahAli Mohammadian Mosammam

Abstract

Because the rice genome has been sequenced entirely, search to find specific features at genome-wide scale is of high importance. Palindromic sequences are important DNA motifs involved in the regulation of different cellular processes and are a potential source of genetic instability. In order to search and study the long palindromic regions in the rice genome “R” statistical programming language was used. All palindromes, defined as identical inverted repeats with spacer DNA, could be analyzed and sorted according to their frequency, size, GC content, compact index etc. The results showed that the overall palindrome frequency was high in rice genome (nearly 51000 palindromes), with highest and lowest number of palindromes, respectively belongs to chromosome 1 and 12. Palindrome numbers could well explain the rice chromosome expansion (R2>92%). Average GC content of the palindromic sequences is 42.1%, indicating AT-richness and hence, the low-complexity of palindromic sequences. The results also showed different compact indices of palindromes in different chromosomes (43.2 per cM in chromosome 8 and 34.5 per cM in chromosome 3, as highest and lowest, respectively). The possible application of palindrome identification can be t...Continue Reading

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Mentioned in this Paper

Directed Evolution
Biological Markers
Genome-Wide Association Study
Chromosomes, Human, Pair 1
Size
Cellular Process
Genome
Malignant Neoplasm of Stomach
Regulation of Biological Process
NRF1 gene

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