title: Evolutionary changes in vertebrate genome signatures with special focus on coelacanth.
abstract: With a remarkable increase in genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-organizing map (SOM) is a powerful tool for clustering high-dimensional data on one plane. For oligonucleotide compositions handled as high-dimensional data, we have previously modified the conventional SOM for genome informatics: BLSOM. In the present study, we constructed BLSOMs for oligonucleotide compositions in fragment sequences (e.g. 100 kb) from a wide range of vertebrates, including coelacanth, and found that the sequences were clustered primarily according to species without species information. As one of the nearest living relatives of tetrapod ancestors, coelacanth is believed to provide access to the phenotypic and genomic transitions leading to the emergence of tetrapods. The characteristic oligonucleotide composition found for coelacanth was connected with the lowest dinucleotide CG occurrence (i.e. the highest CG suppression) among fishes, which was rather equivalent to that of tetrapods. This evident CG suppression in coelacanth should reflect molecular evolutionary processes of epigenetic systems including DNA methylation during vertebrate evolution. Sequence of a de novo DNA methylase (Dntm3a) of coelacanth was found to be more closely related to that of tetrapods than that of other fishes.
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Iwasaki
authors.affiliation: Department of Information Engineering, Faculty of Engineering, Institute of Science and Technology, Niigata University, Niigata-ken 950-2181, Japan takaabe@ie.niigata-u.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226, Japan Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Norihiro
authors.initials: N
authors.lastname: Okada
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
authors.forename: Kennosuke
authors.initials: K
authors.lastname: Wada
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Wada
authors.affiliation: Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
mesh_terms: D000818:Animals; D019295:Computational Biology; D015254:DNA Modification Methylases / Q000235:genetics; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics; D016678:Genome; D010802:Phylogeny; D014714:Vertebrates / Q000235:genetics*
chemical_list: D015254:DNA Modification Methylases
keywords: CG suppression; DNA methylation; SOM; big data; epigenetic