The Rice Word Landscape: A Detailed Catalogue of the Rice Motif Content in the Non-coding Regions

Abstract

Among the different areas of molecular biology concerning the detailed study of different parts of the cell, such as genomics, proteomics, and metabolomics, different new areas of study are emerging which entail the analysis of different parts of the genome, such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study was to construct and analyze a catalogue of all statistically relevant putative functional octamer words or motifs (which we have termed the "motifome" of a given organism) found within first introns, promoters, the 5' and 3' untranslated regions (UTRs), and the entire genome of japonica rice, and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of non-coding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. While common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.

K-mer-Based Motif Analysis in Insect Species across Anopheles, Drosophila, and Glossina Genera and Its Application to Species Classification

“…The original k-mer scoring algorithm was described in the study of Lichtenberg et al [21] and Cserhati et al [1]. The algorithm is briefly described below; however, more details on the mathematical background for scoring the significance of a given k-mer can be found in the original publications.…”

“…These elements are both conserved and diverged across species owing to their functional significance, which enables these k-mer signatures ideal for species identification. Several recent studies have described the distribution of statistically significant k-mers in the genomes and several regulatory subregions (core, proximal, distal promoters, and 3′ and 5′ UTRs) in a small number of plant species as well as modern and archaic humans [1–3]. A k-mer is a type of short oligonucleotide of length k. K-mers can be part of core segments of transcription factor binding sites or regulatory elements that take part in protein binding and gene regulation in different subregions of the genome.…”

“…Compared to our previous work in this area [1–3], the current improved algorithm scores k-mer significance based on a normalized scale of −1 to +1, which is used to calculate k-mer signatures so as not only to predict statistically significant and biologically relevant k-mers, but also to make the genomes of two given species comparable based on their k-mer signatures. Therefore, the goal of this study is to further develop a k-mer prediction method, which can be used to predict biologically significant k-mers and then to use these k-mers in species comparison and clustering.…”