title: Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.
abstract: A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.
authors.affiliation: Information Engineering, Niigata University, Niigata-shi, Niigata-ken 950-2181, Japan.
authors.forename: Takashi
authors.identifier: 0000-0002-8692-4241
authors.initials: T
authors.lastname: Abe
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma-shi, Nara-ken 630-0101, Japan ; Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan.
authors.forename: Yuta
authors.initials: Y
authors.lastname: Hamano
authors.affiliation: Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan.
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D004330:Drosophila / Q000235:genetics*; D016678:Genome / Q000502:physiology*; D010802:Phylogeny; D013045:Species Specificity
references.citation: Nucleic Acids Res. 1984 Feb 10;12(3):1749-63
references.pmid: 6583663
references.citation: PLoS Genet. 2007 Nov;3(11):e197
references.pmid: 17997610
references.citation: Nucleic Acids Res. 1987 Mar 25;15(6):2611-26
references.pmid: 3550699
references.citation: ISME J. 2013 May;7(5):1003-15
references.pmid: 23303373
references.citation: Curr Opin Microbiol. 1998 Oct;1(5):598-610
references.pmid: 10066522
references.citation: Genome Res. 2001 Apr;11(4):540-6
references.pmid: 11282969
references.citation: Nature. 2007 Nov 8;450(7167):203-18
references.pmid: 17994087
references.citation: J Bacteriol. 1997 Jun;179(12):3899-913
references.pmid: 9190805
references.citation: Genome Res. 2003 Apr;13(4):693-702
references.pmid: 12671005
references.citation: DNA Res. 2005;12(5):281-90
references.pmid: 16769690
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Nucleic Acids Res. 1998 Jun 15;26(12):2971-80
references.pmid: 9611243
references.citation: DNA Res. 2009 Oct;16(5):287-97
references.pmid: 19801558
references.citation: Gene. 2001 Oct 3;276(1-2):89-99
references.pmid: 11591475
references.citation: Annu Rev Genet. 1998;32:185-225
references.pmid: 9928479
references.citation: Gene. 2006 Jan 3;365:27-34
references.pmid: 16364569
references.citation: Nature. 2007 Nov 8;450(7167):219-32
references.pmid: 17994088
references.citation: Chromosome Res. 2013 Aug;21(5):461-74
references.pmid: 23896648