Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 30-42 |
| Number of pages | 13 |
| Journal | Genomics |
| Volume | 106 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jul 1 2015 |
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Keywords
- Genome distance
- Genome signature
- Genome visualization
- Genome-scale classification
- Microbial genomes
- Repetitive element
ASJC Scopus subject areas
- Genetics
Cite this
Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes. / Lee, Kang Hoon; Shin, Kyung Seop; Lim, Debora; Kim, Woo Chan; Chung, Byung Chang; Han, Gyu Bum; Roh, Jeongkyu; Cho, Dong Ho; Cho, Kiho.
In: Genomics, Vol. 106, No. 1, 01.07.2015, p. 30-42.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes
AU - Lee, Kang Hoon
AU - Shin, Kyung Seop
AU - Lim, Debora
AU - Kim, Woo Chan
AU - Chung, Byung Chang
AU - Han, Gyu Bum
AU - Roh, Jeongkyu
AU - Cho, Dong Ho
AU - Cho, Kiho
PY - 2015/7/1
Y1 - 2015/7/1
N2 - 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.
AB - 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.
KW - Genome distance
KW - Genome signature
KW - Genome visualization
KW - Genome-scale classification
KW - Microbial genomes
KW - Repetitive element
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U2 - 10.1016/j.ygeno.2015.04.004
DO - 10.1016/j.ygeno.2015.04.004
M3 - Article
VL - 106
SP - 30
EP - 42
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 1
ER -