Comparing the Human and Fish Genomes

Abstract

Comparing human and fish genomes has been proven useful to understand vertebrate evolution. To demonstrate this, two major questions and related findings are addressed here. In 1970, based on limited observations, Ohno postulated that whole genome duplication events took place in early vertebrates and were essential to increasing complexity of vertebrates over the past 600 My. For providing conclusive support to Ohno's hypothesis, comparative genomics of the fish and human genomes was indispensable. Another question is whether deoxyribonucleic acid (DNA) sequence variation might reflect germ line genetic activity, underlying chromatin structure and DNA methylation. Analysis of the medaka fish and human genomes uncovered two important properties. Nucleosome positioning is correlated with periodic sequence variation downstream of transcription start sites in germ line cells, and genome‐wide genetic variations are highly correlated with proximal DNA methylation patterns. These findings suggest the potential for genetic activity (transcription), chromatin structure and DNA methylation to contribute to moudling the DNA sequence on an evolutionary timescale. Key Concepts: In 1970, based on limited observations, Ohno postulated that whole genome duplication events took place in early vertebrates and were essential to increasing complexity of vertebrates over the past 600 My. Comparative genomics of the fish and human genomes was indispensable to provide conclusive support to Ohno's hypothesis. Nucleosome positioning is correlated with periodic sequence variation downstream of transcription start sites in germ line cells. Genome‐wide genetic variations are highly correlated with proximal DNA methylation patterns. Nakatani et al. suggest a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage‐specific genome reorganisations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.