Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

Abstract

Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate that researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate preduplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish. However, we find that the early vertebrate WGD events were not followed by increased rates of genome rearrangement. Indeed, we measure massive genome rearrangement prior to these WGD events. We propose that the vertebrate WGD events may have been symptoms of a preexisting predisposition toward genomic structural change.

Characterization of drCol 15a1b: A Novel Component of the Stem Cell Niche in the Zebrafish Retina

“…Edge lengths are scaled by the number of trees in which that split is present. occurred along lineages known to contain whole genome duplication (WGD) events (two along the ancestral vertebrate lineage and one along the ancestral teleost lineage [49,50]. Therefore, all three duplications within the collagen XV/ XVIII family may have occurred as part of WGD events, and not as a result of a ''segmental duplication'' (relatively large duplications of genomic regions <1 kb, including both tandemly and nontandemly repeated regions [51]).…”

How life changes itself: The Read–Write (RW) genome

“…WGD can happen at very high frequencies (25% of all hybrids in a recent Arabidopsis study [129]). In our own ancestry, there were two successive WGD events at the beginning of vertebrate evolution [130][131][132].…”

Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

“…For example, teleosts have experienced a higher rate of gene-linkage disruption and chromosomal rearrangements (Kasahara et al, 2007;Semon and Wolfe, 2007a;Venkatesh et al, 2007;Hufton et al, 2008), faster evolution of protein-coding sequences (Robinson-Rechavi and Laudet, 2001;Jaillon et al, 2004;Brunet et al, 2006) and conserved noncoding elements (CNEs) (Chiu et al, 2002;Venkatesh et al, 2006) compared to cartilaginous fishes and mammals, and have a large number of teleost lineage-specific genes (Yang et al, 2013). The potential implications of these processes in the diversification and rapid speciation of teleost fishes have been extensively discussed (Ravi and Venkatesh, 2008;Yang et al, 2013).…”