Genome duplication, a trait shared by 22000 species of ray-finned fish.

By J. Taylor, I. Braasch, T. Frickey, Axel Meyer, Y. Van de Peer. Genome Research, 2003

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Through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies in the tetraploid frog Xenopus laevis, and two copies in zebrafish (Danio rerio). For 22 of these genes, both zebrafish duplicates had orthologs in the pufferfish (Takifugu rubripes). For another 20 of these genes, we found only one pufferfish ortholog but in each case it was more closely related to one of the zebrafish duplicates than to the other. Forty-three pairs of duplicated genes map to 24 of the 25 zebrafish linkage groups but they are not randomly distributed; we identified 10 duplicated regions of the zebrafish genome that each contain between two and five sets of paralogous genes. These phylogeny and synteny data suggest that the common ancestor of zebrafish and pufferfish, a fish that gave rise to approximately 22000 species, experienced a large-scale gene or complete genome duplication event and that the pufferfish has lost many duplicates that the zebrafish has retained.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/19402270d5e0e38d5c2e71ed8551f2f1631b7c6d

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Citations in the corpus

Duplication and divergence: the evolution of new genes and old ideas. (2004, background): “The analysis of whole-genome sequences has turned up evidence for ancient genome duplication in yeast (Saccharomyces cerevisiae) (67, 110, 140, 142), Arabidopsis thaliania (10–12, 27, 106, 115, 133), and fish (125, 129), aneuploidy in rice (Oryza sativa spp.”
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species (2018, background): “A case for lineage-specific genomic features to promote speciation has for instance been made for ray-finned fishes (e.g. Taylor et al., 2003; Venkatesh, 2003; Rennison, Owens & Taylor, 2012; Cortesi et al., 2015).”
Teleost fish with specific genome duplication as unique models of vertebrate evolution (2010, background): “accumulating data from molecular and genome biology (Ohno 1999; Abi-Rached et al. 2002; Furlong and Holland 2002; Taylor et al. 2003).”
Evolution of alternative sex-determining mechanisms in teleost fishes (2006, background): “…a fast pace of genic and genomic duplication (Robinson-Rechavi & Laudet, 2001; Robinson-Rechavi et al., 2001), both recent (Allendorf & Thorgaard, 1984; Ferris, 1984; Vandepoele et al., 2004) and ancient (Amores et al., 1998; Taylor et al., 2003), has been documented in the ray-finned fishes.”
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). (2005, background): “The observations that different paralogous pairs seem to have originated at about the same time,((31)) that different ray-finned fish species seem to share ancient gene duplications((32)) and that different paralogs are found on different linkage groups and show synteny with other duplicated chromos”
Adaptive, pre-adaptive and non-adaptive components of radiations in ancient lakes: a review (2004, background): “Reproductive modes mostly cited are: (1) mouth brooding and philopatry, as well as homing and home-site fidelity in cichlids, all of which considerably affect the genetic population structure (Taylor et al. 2001); (2) brooding in general, e.”
Occurrence of polyploidy in the fishes (2003, background): “…in the literature (Ohno, 1970; Ferris and Whitt, 1979; Li, 1980; Allendorf and Thorgaard, 1984; Larhammar and Risinger, 1994; Wittbrodt et al., 1998; Aparicio, 2000; Otto and Whitton, 2000; Taylor et al., 2003), this represents a process that takes place in established polyploid species (Li, 1980).”
Whole-genome duplication in teleost fishes and its evolutionary consequences (2014, background): “Since the conservation of long stretches of gene order in the entire teleost lineage is an expected outcome of a WGD, the detection of conserved synteny (gene order on chromosomes) of Hox clusters and other genes in a number of teleost fishes was taken as strong evidence for TS-WGD (Amores et al. 19”
Molecular evolution of a microRNA cluster. (2004, background): “It is very likely, however, that at least the teleost I-A and I-B clusters arose during the teleost-specific genome duplication.(24) The homology of Dr14 Figure 5.”
Polyploidy in Fish and the Teleost Genome Duplication (2012, background): “rubripes) revealed that these fish-specific gene duplications within multigene families usually date back to a point during rayfin fish evolution before the divergence of zebrafish and pufferfish (Amores et al. 1998; Postlethwait et al. 2002; Taylor et al. 2003).”