Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.

By Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita. 2007

487 citations recorded by the source corpus.

Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

Subfields: Genetics, Molecular Biology, Plant Science

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Citations in the corpus

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity (2012, background): “In contrast, karyotype evolution among major vertebrate lineages appears to have been slower, with a single whole-genome duplication event 500million years ago (4,7).”
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes (2008, unknown): “annotated orthologous genes [10,22,35,36], to whole genome”
Biased gene conversion and the evolution of mammalian genomic landscapes. (2009, background): “In mammals, although the genome size is nearly constant, the number (and hence size) of chromosomes has evolved rapidly as a result of frequent chromosomal rearrangements (104).”
Polyploidy in Fish and the Teleost Genome Duplication (2012, background): “Using several teleost genetic maps as well as the genome assemblies of Tetraodon and medaka, several attempts have been made to reconstruct the ancestral pre-TGD protokaryotype (Naruse et al. 2004; Jaillon et al. 2004; Woods et al. 2005; Kohn et al. 2006; Kasahara et al. 2007; Nakatani et al. 2007).”
Teleost fish with specific genome duplication as unique models of vertebrate evolution (2010, background): “4 of Kasahara et al. 2007), probably via many inter-chromosome translocations, fissions (Nakatani et al. 2007), and segmental duplications (International Human Genome Sequencing Consortium 2004).”
Genome duplication in amphibians and fish: an extended synthesis (2011, methodology): “Recent analyses of whole genome sequences and ancestral reconstruction suggest that the ancestor of all teleost fishes had a haploid chromosome complement of 12–13 chromosomes that increased to 23–24 chromosomes after the teleost-specific duplication (Jaillon et al., 2004; Kasahara et al., 2007; Nak”