Comparative genomics - Small genome, big insights

University of Oxford, Oxford, England, United Kingdom
Nature (Impact Factor: 41.46). 11/2004; 431(7011):916-7. DOI: 10.1038/431916a
Source: PubMed


The genome of a second pufferfish species has been sequenced. Why is this important? Because comparing this genome with that of other animals yields a wealth of information on genome evolution.

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Available from: Peter Holland, Sep 10, 2014
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    • "In addition to these 6 STATs, the zebrafish has acquired two extra orthologous STATs, one similar to STAT1 and the other similar to STAT5 (Fig. 4). These extra STATs were likely gained through the whole genome duplication that occurred early in teleost evolution after divergence from the tetrapods,31,32 and thus unlikely to be present in their common ancestor with the mammals. These duplicated STATs may have survived due to expression pattern diversification, similar to the duplicated zebrafish JAK2.33 Furthermore, they were likely lost in the pufferfish lineage, presumably in favor of a much more compact genome. "
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    ABSTRACT: The STAT signaling pathway is one of the seven common pathways that govern cell fate decisions during animal development. Comparative genomics revealed multiple incidences of stat gene duplications throughout metazoan evolutionary history. While pseudogenization is a frequent fate of duplicated genes, many of these STAT duplications evolved into novel genes through rapid sequence diversification and neofunctionalization. Additionally, the core of STAT gene regulatory networks, comprising stat1 through 4, stat5 and stat6, arose early in vertebrate evolution, probably through the two whole genome duplication events that occurred after the split of Cephalochordates but before the rise of Chondrichthyes. While another complete genome duplication event took place during the evolution of bony fish after their separation from the tetrapods about 450 million years ago (Mya), modern fish have only one set of these core stats, suggesting the rapid loss of most duplicated stat genes. The two stat5 genes in mammals likely arose from a duplication event in early Eutherian evolution, a period from about 310 Mya at the avian-mammal divergence to the separation of marsupials from other mammals about 130 Mya. These analyses indicate that whole genome duplications and gene duplications by unequal chromosomal crossing over were likely the major mechanisms underlying the evolution of STATs.
    01/2012; 1(1):23-33. DOI:10.4161/jkst.19418
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    • "Although vertebrates from pufferfish to humans share a similar gene inventory, recent analyses demonstrated that a WGD occurred before the divergence of teleosts and osteoglossomorphs more than 230–350 million years ago, whereas other ray-finned fish (actinopterygians) and all sarcopterygians (tetrapods and coelacanthiforms) experienced no such event [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47]. As tetraploidy was deleterious and strongly selected against, the duplicated genomes in the tetraploid teleost ancestor eventually coalesced in a process called diploidization [3], [48], [49], [50], [51]. "
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    ABSTRACT: One of the most interesting questions in biology is whether certain pathways have been favored during evolution, and if so, what properties could cause such a preference. Due to the lack of experimental evidence, whether select gene families have been preferentially retained over time after duplication in metazoan organisms remains unclear. Here, by syntenic mapping of nonchemosensory G protein-coupled receptor genes (nGPCRs which represent half the receptome for transmembrane signaling) in the vertebrate genomes, we found that, as opposed to the 8-15% retention rate for whole genome duplication (WGD)-derived gene duplicates in the entire genome of pufferfish, greater than 27.8% of WGD-derived nGPCRs which interact with a nonpeptide ligand were retained after WGD in pufferfish Tetraodon nigroviridis. In addition, we show that concurrent duplication of cognate ligand genes by WGD could impose selection of nGPCRs that interact with a polypeptide ligand. Against less than 2.25% probability for parallel retention of a pair of WGD-derived ligands and a pair of cognate receptor duplicates, we found a more than 8.9% retention of WGD-derived ligand-nGPCR pairs--threefold greater than one would surmise. These results demonstrate that gene retention is not uniform after WGD in vertebrates, and suggest a Darwinian selection of GPCR-mediated intercellular communication in metazoan organisms.
    PLoS ONE 02/2008; 3(4):e1903. DOI:10.1371/journal.pone.0001903 · 3.23 Impact Factor
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    • "The ascidian Ciona is included in addition to the other 2 model representatives of invertebrate species because it occupies a unique evolutionary position as an invertebrate chordate, bridging between the vertebrate and invertebrate lineages, and hence sharing properties with both lineages. Moreover, its gene complement can be regarded as a first approximation to the ancestral chordate complement (Mulley and Holland 2004). With the vertebrate GRL genes, there is considerable similarity in number, gene structure, and chromosomal arrangement between fish, avian, and mammals. "
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    ABSTRACT: The inhibitory ligand-gated ion channel family of receptors, including the type A gamma-aminobutryic acid (GABA(A)) and glycine receptors, mediates inhibitory neurotransmissions in the central nervous system. In this study, GABA receptor (GABR) evolution was explored through comparative genomics using genomes that span divergent lineages. GABA(A)/Gly receptor-like (GRL) gene sequences were retrieved from the genomes of various species ranging from mammal to fish to worm and subjected to cross-species comparison. All vertebrate GRL gene sets in the study but no invertebrate ones exhibit the extensive and conserved pattern of gene clustering that is characteristic of human GABR genes, indicating that the gene clusters were established early in vertebrate evolution, after divergence from the invertebrates. Moreover, the vertebrate gene structure is highly conserved with a basic 9-coding exon structure, whereas, as well as being diverse in copy numbers and chromosomal loci, the invertebrate GRL genes display a variety of gene structures. Remarkably, the invertebrates each possess a unique GRL gene pair that lies in neighboring loci within their respective genomes: zc482.5 and zc482.1 in roundworm, CG8916 and CG17336 in fruitfly, Ci4249 and Ci4254 in Ciona, and these were revealed by phylogenetic analysis to be homologous to human GABR alpha and beta subunits, respectively. The phylogenetic classification of these genes is also corroborated by experimental ligand-binding measurements using recombinant gene products. Furthermore, the 3 invertebrate gene pairs harbor characteristic key residues and exhibit similarities in intron positions to their vertebrate counterparts. The results strongly indicate that such a gene pair originally existed in the bilaterian ancestor from which all 3 phyla evolved and suggest that the extant GABR clusters arose from an ancestral alpha-beta subunit gene pair gave rise to the extant GABR clusters.
    Molecular Biology and Evolution 03/2007; 24(2):599-610. DOI:10.1093/molbev/msl188 · 9.11 Impact Factor
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