Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth

Witharemarkableincreaseingenomicsequencedataofawiderangeofspecies,noveltoolsareneededfor comprehensiveanalysesofthebigsequencedata.Self-organizingmap(SOM)isapowerfultoolforclustering high-dimensionaldataononeplane.Foroligonucleotidecompositionshandledashigh-dimensionaldata,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 rangeofvertebrates,includingcoelacanth,andfoundthatthesequenceswereclusteredprimarilyaccording 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 lowestdinucleotide CG occurrence(i.e. the highest CG suppression) amongfishes, which was ratherequivalent 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.