Evolution and Diversity of Fish Genomes Venkatesh 589
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588 Evolution and diversity of fish genomes Byrappa Venkatesh The ray-finned fishes (‘fishes’) vary widely in genome size, Although traditionally fishes have been the subject morphology and adaptations. Teleosts, which comprise 23,600 of comparative studies, recently there has been an species, constitute >99% of living fishes. The radiation of increased interest in these vertebrates as model organ- teleosts has been attributed to a genome duplication event, isms in genomics and molecular genetics. Indeed, the which is proposed to have occurred in an ancient teleost. But second vertebrate genome to be sequenced completely more evidence is required to support the genome-duplication was that of a pufferfish (Fugu rubripes) [4], the first being hypothesis and to establish a causal relationship between the human genome. The genome of another pufferfish additional genes and teleost diversity. Fish genomes seem to be (Tetraodon nigroviridis) is essentially complete, and that ‘plastic’ in comparison with other vertebrate genomes because of the zebrafish (Danio rerio) is nearing completion. The genetic changes, such as polyploidization, gene duplications, genome of a fourth fish, medaka (Oryzias latipes), is also gain of spliceosomal introns and speciation, are more being sequenced. frequent in fishes. The analyses of the fish genome sequences have provided Addresses useful information for understanding the structure, func- Institute of Molecular and Cell Biology 30, Medical Drive, Singapore tion and evolution of vertebrate genes and genomes. In 117609, Singapore this review, I discuss the insights gained from recent e-mail: [email protected] studies on the evolution of fish genomes. Current Opinion in Genetics & Development 2003, 13:588–592 Genome size of fishes Fish genomes vary widely in size, from 0.39 pg to >5 pg of This review comes from a themed issue on DNA per haploid cell (Figure 2), with a modal value of Genomes and evolution 1 pg (equivalent to 1000 Mb). Most of the large gen- Edited by Evan Eichler and Nipam Patel omes (>2 pg) are polyploids. Among vertebrates, poly- 0959-437X/$ – see front matter ploidization is common only in fishes, amphibians and ß 2003 Elsevier Ltd. All rights reserved. reptiles. In fishes, polyploidization has occurred indepen- dently in several lineages including non-teleosts such as DOI 10.1016/j.gde.2003.09.001 the paddlefish, shovelnose sturgeon and spotted gar, as well as teleosts such as cyprinids (carps), cyprinodonti- Abbreviation formes (live bearers), catostomids (suckers) and salmo- My million years nids [5,6]. In fact, all members of the families Catostomidae and Salmonidae are polyploids [5,6]. Introduction The pufferfish — family Tetraodontidae, including, for The ray-finned fishes, which comprise 23,700 extant example, Fugu and Tetraodon — have the smallest gen- species [1], are the most diverse and successful group of omes among vertebrates that have been characterized to vertebrates. They show vast differences in their morphol- date. Their genomes therefore offer an interesting model ogy and adaptations. Their sister group, the lobe-finned for understanding the evolutionary forces that lead to a fishes, include the rest of the bony vertebrates, such as reduction in genome size. A paucity of repetitive elements coelacanths, lungfishes and tetrapods, and are repre- is clearly one of the factors that contributes to the compact sented by 23,600 living species (Figure 1). The two genome size of pufferfish. Interestingly, although the bony vertebrate lineages diverged 450 million years repetitive sequences account for <15% of the Fugu gen- (My) ago [2]. The ray-finned fishes (‘fishes’) can be ome, almost every class of transposable elements known subdivided into the basal ‘non-teleosts’, represented by in eukaryotes is represented in Fugu. Furthermore, a large four major lineages: Polypteriformes (bichirs), Acipenser- number of transposable elements (40 families as com- iformes (sturgeons and paddlefish), Semionotiformes pared with 6 in the human genome) seem to be of recent (gar) and Amiiformes (bowfin); and the higher teleosts. origin, as they have accumulated substitutions at a level of Teleosts are the largest group of vertebrates and comprise <5% [4]. This indicates that the pufferfish genome is 23,600 species. The most ancient teleost fossil is 235 susceptible to transposable elements, but the propagation My old [3], and fossils of diverse teleost species have been of these elements is somehow restricted. recorded from Jurassic and Cretaceous times. Thus, tele- osts appear to have undergone a rapid radiation that is Interspersed repeats of the same divergence level in Fugu unparalleled in other vertebrate taxa. and humans have more small internal deletions in Fugu Current Opinion in Genetics & Development 2003, 13:588–592 www.current-opinion.com Evolution and diversity of fish genomes Venkatesh 589 Figure 1 Number of living species Mammals 310 Birds ods 23,550 360 Reptiles Tetrap Amphibians Lobe-finned fish Lobe-finned Lungfishes 6 Coelacanths 2 450 Non-teleosts 44 >235 Teleosts 23,637 fish Ray-finned Current Opinion in Genetics & Development Evolution of bony vertebrates. ‘Non-teleosts’ is not a taxonomic group: it includes the basal groups Polypteriformes, Acipenseriformes, Semionotiformes and Amiiformes, which are not teleosts. The numbers at the nodes are the divergence time in million years [2]. There is no reliable estimate for the divergence time of teleosts, but the oldest fossil record of teleosts is 235 My old [3]. The data on numbers of living species are from [1]. A whole-genome duplication has been proposed to have occurred in an ancient teleost (indicated by arrow). than in humans [4], indicating that deletions occur at a dundant genes, and probably accounts for the lower abun- higher rate in Fugu. Similarly, the overall frequency of dance of such sequences in pufferfish than in mammals. small deletions in pseudogenes has been found to be higher in another pufferfish, Tetraodon, than in mammals In addition to DNA loss, these pufferfish (referred to as [7]. Such a bias for DNA loss provides a mechanism for ‘smooth puffers’) seem to be subject to other mechanisms inactivating and deleting transposable elements and re- that minimize their genomes. For example, comparisons Figure 2 70 60 Medaka 50 40 30 20 Number of species Goldfish Zebrafish 10 Fugu Rainbow trout 0 >3.51 0.31–0.4 0.51–0.6 0.71–0.8 0.91–1.0 1.11–1.2 1.31–1.4 1.51–1.6 1.71–1.8 1.91–2.0 2.11–2.2 2.31–2.4 2.51–2.6 2.71–2.8 2.91–3.0 3.11–3.2 3.31–3.4 Genome size (pg DNA/haploid cell) Current Opinion in Genetics & Development Distribution of genome size of fishes. Genome size is given in picograms of DNA per haploid cell: 1 pg of DNA is roughly equivalent to 1000 Mb. Genome sizes of 312 species [8,42,43] belonging to 30 of the known 42 orders of fishes are represented. Only one representative species for each genera is included. www.current-opinion.com Current Opinion in Genetics & Development 2003, 13:588–592 590 Genomes and evolution of mutation profiles between the smooth puffers To date, gene-duplication studies in fishes are limited to a (Tetraodontidae) and their sister group the spiny puffers small number of gene loci in only a few species. Thus, to (Diodontidae), whose genome size (800 Mb) is twice generate strong statistical evidence, it is necessary to that of the smooth puffers [8], suggest that a reduction in investigate duplication events in a large number of loci the rate of large insertions — rather than an increase in in diverse lineages, including a basal lineage. Compar- large deletions — was the probable cause of the reduction isons of the completed genome sequences of Fugu — the in the genome size of the smooth puffers after they present ‘draft’ is in the form of 12,000 fragments and lacks diverged from the spiny puffers [9]. Thus, besides a chromosome coordinates — and other teleosts that are high rate of DNA loss, bias against insertion of large DNA being sequenced should provide useful data for tracing elements may be responsible for the ‘smallest vertebrate’ the history of duplications. genomes of the smooth puffers. Duplicate genes and teleost radiation Gene duplications in fishes It has been suggested that the vast morphological and Since the first identification of additional Hox gene clus- species diversity of teleosts might be related to large-scale ters in diploid teleosts such as zebrafish, Fugu and medaka independent gene duplications or to a whole-genome [10–12], other additional duplicate genes have been iden- duplication in an ancient teleost [10,27,28]. After gene tified in these and other teleosts [13–24,25].Manyofthe duplication, either one of the duplicates is silenced and duplicate genes in zebrafish and Fugu map to similar pairs eliminated, or both of the duplicates are retained through of chromosome segments, suggesting that they arose as a mutations that divide the functions between the two or result of large-segment or whole-chromosome duplica- that confer a novel function on one of them. Contrary to tions [22,24,25,26,27]. Furthermore, orthologs for 22 previous thinking that silencing of a duplicate gene copy of the 49 pairs of duplicate zebrafish genes have been has no consequence for the species, the recently proposed identified in the Fugu [27]. These observations have led ‘reciprocal silencing’ and ‘divergent resolution’ models to the hypothesis that a whole-genome duplication show that the silencing of different copies of duplicate occurred in an ancestor common to the Fugu and zebrafish genes in allopatric populations can genetically isolate lineages [10,20,27]. Because zebrafish and Fugu are populations, thereby spurring speciation [29,30]. Further- phylogenetically distant (they are grouped under the more, different subfunctionalization patterns of dupli- subdivision Euteleostei, which includes >90% of extant cates in different populations can also lead, like gene teleost species), it has been proposed that the duplication silencing, to genetic isolation [30].