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 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.
Department of Surgery, University of California, Davis, Sacramento, CA, United States; Shriners Hospitals for Children Northern California, Sacramento, CA, United States.
Kang-Hoon
KH
Lee
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Kyung-Seop
KS
Shin
Department of Surgery, University of California, Davis, Sacramento, CA, United States; Shriners Hospitals for Children Northern California, Sacramento, CA, United States.
Debora
D
Lim
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Woo-Chan
WC
Kim
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Byung Chang
BC
Chung
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Gyu-Bum
GB
Han
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Jeongkyu
J
Roh
Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
Dong-Ho
DH
Cho
Department of Surgery, University of California, Davis, Sacramento, CA, United States; Shriners Hospitals for Children Northern California, Sacramento, CA, United States. Electronic address: kcho@ucdavis.edu.
Kiho
K
Cho
D000465:Algorithms; D016000:Cluster Analysis; D004247:DNA / Q000737:chemistry; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D020125:Mutation, Missense; D012091:Repetitive Sequences, Nucleic Acid
D004247:DNA
Genome distance; Genome signature; Genome visualization; Genome-scale classification; Microbial genomes; Repetitive element