Molecular evolution in the lamprey genomes and its relevance to the timing of whole genome duplications

Abstract

The genomes of two lamprey species have been sequenced, and this has provided the basis for genome-wide comparison of molecular evolution between jawless fishes and the rest of vertebrates. Molecular phylogenetic analyses of jawless fish genes increased our knowledge of the evolutionary time scale of diversification of hagfishes and lampreys, as well as of gene redundancy in their genomes. It was shown that the ancestor of jawed vertebrates experienced two rounds of whole genome duplications (Dehal & Boore, 2005). However, it has been controversial whether this event occurred before or after the ancestors of extant jawless fishes diverged from the lineage which gave rise to jawed vertebrates (e.g., Escriva et al., 2002; reviewed in Kuraku, 2013). Recent molecular phylogenetic studies showed that the whole genome duplications occurred before the radiation of all extant vertebrates including hagfishes and lampreys (Kuraku et al., 2009a), and this scenario has been confirmed by later studies including the genomic analysis of Petromyzon marinus (sea lamprey) (Hoffmann et al., 2010; Smith et al., 2013). In this chapter, we analyze peculiar characteristics of the lamprey genomes, focusing mainly on protein-coding regions, to propose potential factors that act as barriers to the understanding of the timing of whole genome duplications.