1 October 2008 Insights into Cyclostome Phylogenomics: Pre-2R or Post-2R
Shigehiro Kuraku
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Interest in understanding the transition from prevertebrates to vertebrates at the molecular level has resulted in accumulating genomic and transcriptomic sequence data for the earliest groups of extant vertebrates, namely, hagfishes (Myxiniformes) and lampreys (Petromyzontiformes). Molecular phylogenetic studies on species phylogeny have revealed the monophyly of cyclostomes and the deep divergence between hagfishes and lampreys (more than 400 million years). In parallel, recent molecular phylogenetic studies have shed light on the complex evolution of the cyclostome genome. This consists of whole genome duplications, shared at least partly with gnathostomes (jawed vertebrates), and cyclostome lineage-specific secondary modifications of the genome, such as gene gains and losses. Therefore, the analysis of cyclostome genomes requires caution in distinguishing between orthology and paralogy in gene molecular phylogeny at the gene family scale, as well as between apomorphic and plesiomorphic genomic traits in larger-scale analyses. In this review, we propose possible ways of improving the resolvability of these evolutionary events, and discuss probable scenarios for cyclostome genome evolution, with special emphasis on the hypothesis that two-round (2R) genome duplication events occurred before the divergence between cyclostomes and gnathostomes, and therefore that a post-2R state is a genomic synapomorphy for all extant vertebrates.

Shigehiro Kuraku "Insights into Cyclostome Phylogenomics: Pre-2R or Post-2R," Zoological Science 25(10), 960-968, (1 October 2008). https://doi.org/10.2108/zsj.25.960
Received: 24 April 2008; Accepted: 1 June 2008; Published: 1 October 2008
hidden paralogy
long branch attraction
whole genome duplication
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