Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes

The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2015-07, Vol.106 (1), p.30-42
Main Authors: Lee, Kang-Hoon, Shin, Kyung-Seop, Lim, Debora, Kim, Woo-Chan, Chung, Byung Chang, Han, Gyu-Bum, Roh, Jeongkyu, Cho, Dong-Ho, Cho, Kiho
Format: Article
Language:English
Subjects:
Algorithms
Archaea
Cluster Analysis
DNA - chemistry
Evolution, Molecular
Genome distance
Genome signature
Genome visualization
Genome, Archaeal
Genome, Bacterial
Genome-scale classification
Genomics - methods
Microbial genomes
Mutation, Missense
Repetitive element
Repetitive Sequences, Nucleic Acid
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Summary:The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme. An algorithm for computing distances among GSIs was formulated using the GSIs' variables (word identity, frequency, and frequency order). The utility of the GSI-distance computation system was demonstrated with control genomes. GSI-based computation of genome-relatedness among 1766 microbes (117 archaea and 1649 bacteria) identified their clustering patterns; although the majority paralleled the established classification, some did not. The Genome Signature Imaging system, with its visualization and distance computation functions, enables genome-scale evolutionary studies involving numerous genomes with varying sizes. •Genomes of microbes are visualized by representative repetitive element (RE) sets.•The RE profile-based GSI system is developed for genome-scale evolutionary studies.•The GSI system enables an efficient computing and cataloging of big genome data.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2015.04.004