The Rice Word Landscape—A Detailed Catalog of the Rice Motif Content in the Noncoding Regions

Cserháti, Mátyás; Turóczy, Zoltán; Dudits, Dénes; Györgyey, János

doi:10.1089/omi.2011.0132

Cited by 4 publications

(10 citation statements)

References 19 publications

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“…The detailed method of the algorithm is described in previous works [8] , [9] , [10] . However, a short description will be given in the Materials and methods section.…”

Section: Resultsmentioning

confidence: 99%

“… [9] , however we performed our own analysis on the genome of this plant species, thus we were working with our own Arabidopsis data sets. Since the analysis had already been performed for O. sativa japonica by Cserhati [8] , we simply used the data sets already available for that species. The genomes for eight of the nine species were masked using RepeatMasker [24] in order to purge them of repeat sequences.…”

Section: Methodsmentioning

confidence: 99%

“…We published similar work on rice in a previous paper [8] , and the methodology to find and determine the statistical significance of motifs used in this study is similar to that in previous works [9] , [10] , therefore we refer the reader to these specific references. Furthermore, what makes the present study significant is that it also makes it possible to compare motif content between more or less related species as well as two different groups of plants, monocots and dicots, making it possible to draw further insights from a wider variety of cross-species comparisons.…”

Section: Introductionmentioning

confidence: 96%

“…In this study, we focus on motifs in plants. The total motif content of differing lengths of Arabidopsis thaliana and Oryza sativa japonica has been determined [8] , [9] , which then allowed for cross-species comparison between a dicot and a monocot species. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include Oryza sativa japonica , Oryza sativa indica , Brachypodium distachyon , Zea mays , Triticum aestivum as monocots and A. thaliana , Lotus japonica , Medicago truncatula , and Populus tremula as dicots.…”

Section: Introductionmentioning

confidence: 99%

“…In this study these motifs serve as regulatory signals or transcription factor binding sites in promoters, 1st introns, or UTR sequences. Octamers were studied in our previous study of O. sativa japonica [8] and in [9] of Arabidopsis . Motifs that are 8 bp long are long enough to be both diverse enough and statistically significant at the same time.…”

Section: Introductionmentioning

confidence: 99%

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Motif content comparison between monocot and dicot species

Cserháti

2015

Genomics Data

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While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome) is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice.

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“…The detailed method of the algorithm is described in previous works [8] , [9] , [10] . However, a short description will be given in the Materials and methods section.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Motif content comparison between monocot and dicot species

Cserháti

2015

Genomics Data

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

Cserháti

Xiao

Guda

2019

Computational and Mathematical Methods in Medicine

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Short k-mer sequences from DNA are both conserved and diverged across species owing to their functional significance in speciation, which enables their use in many species classification algorithms. In the present study, we developed a methodology to analyze the DNA k-mers of whole genome, 5′ UTR, intron, and 3′ UTR regions from 58 insect species belonging to three genera of Diptera that include Anopheles, Drosophila, and Glossina. We developed an improved algorithm to predict and score k-mers based on a scheme that normalizes k-mer scores in different genomic subregions. This algorithm takes advantage of the information content of the whole genome as opposed to other algorithms or studies that analyze only a small group of genes. Our algorithm uses k-mers of lengths 7–9 bp for the whole genome, 5′ and 3′ UTR regions as well as the intronic regions. Taxonomical relationships based on the whole-genome k-mer signatures showed that species of the three genera clustered together quite visibly. We also improved the scoring and filtering of these k-mers for accurate species identification. The whole-genome k-mer content correlation algorithm showed that species within a single genus correlated tightly with each other as compared to other genera. The genomes of two Aedes and one Culex species were also analyzed to demonstrate how newly sequenced species can be classified using the algorithm. Furthermore, working with several dozen species has enabled us to assign a whole-genome k-mer signature for each of the 58 Dipteran species by making all-to-all pairwise comparison of the k-mer content. These signatures were used to compare the similarity between species and to identify clusters of species displaying similar signatures.

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Motifome comparison between modern human, Neanderthal and Denisovan

et al. 2018

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BackgroundThe availability of the genomes of two archaic humans, Neanderthal and Denisovan, and that of modern humans provides researchers an opportunity to investigate genetic differences between these three subspecies on a genome-wide scale. Here we describe an algorithm that predicts statistically significant motifs based on the difference between a given motif’s actual and expected distributions. The algorithm was previously applied to plants but was modified for this work.ResultsThe result of applying the algorithm to the human, Neanderthal, and Denisovan genomes is a catalog of potential regulatory motifs in these three human subspecies. We examined the distributions of these motifs in genetic elements including human retroviruses, human accelerated regions, and human accelerated conserved noncoding sequences regions. Differences in these distributions could be the origin of differences in phenotype between the three subspecies. Twenty significant motifs common to all three genomes were found; thirty-three were found in endogenous retroviruses in Neanderthal and Denisovan. Ten of these motifs mapped to the 22 bp core of MiR-1304. The core of this genetic element regulates the ENAM and AMTN genes, which take part in odontogenesis and whose 3’ UTRs contained significant motifs. The introns of 20 genes were found to contain a large number of significant motifs, which were also overrepresented in 49 human accelerated regions. These genes include NAV2, SorCS2, TRAPPC9, GRID1, PRDM16, CAMTA1, and ASIC which are all involved in neuroregulation. Further analysis of these genes using the GO database indicates that many are associated with neurodevelopment. Also, varying numbers of significant motifs were found to occur in regions of the Neanderthal and Denisovan genomes that are missing from the human genome, suggesting further functional differences between modern and archaic humans.ConclusionAlthough Neanderthal and Denisovan are now extinct, detailed examination of elements from their genomes can shed light on possible phenotypic and cognitive differences between these two archaic human subspecies and modern humans. Genetic similarities and differences between these three subspecies and other fossil hominids would also be of interest.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4710-1) contains supplementary material, which is available to authorized users.

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The Rice Word Landscape—A Detailed Catalog of the Rice Motif Content in the Noncoding Regions

Cited by 4 publications

References 19 publications

Motif content comparison between monocot and dicot species

Motif content comparison between monocot and dicot species

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

Motifome comparison between modern human, Neanderthal and Denisovan

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