Patterns of genome size evolution in tetraodontiform fishes

Does genome size increase with water depth in marine fishes?

A growing body of research suggests that genome size in animals can be affected by ecological factors. Half a century ago, Ebeling et al. proposed that genome size increases with depth in some teleost fish groups and discussed a number of biological mechanisms that may explain this pattern (e.g., passive accumulation, adaptive acclimation). Using phylogenetic comparative approaches, we revisit this hypothesis based on genome size and ecological data from up to 708 marine fish species in combination with a set of large-scale phylogenies, including a newly inferred tree. We also conduct modeling approaches of trait evolution and implement a variety of regression analyses to assess the relationship between genome size and depth. Our reanalysis of Ebeling et al.'s dataset shows a weak association between these variables, but the overall pattern in their data is driven by a single clade. Although new analyses based on our "all-species" dataset resulted in positive correlations, providing some evidence that genome size evolves as a function of depth, only one subclade consistently yielded statistically significant correlations. By contrast, negative correlations are rare and nonsignificant. All in all, we find modest evidence for an increase in genome size along the depth axis in marine fishes. We discuss some mechanistic explanations for the observed trends.

A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation

Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.

Genome size estimation of brackishwater fishes and penaeid shrimps by flow cytometry

Flow cytometry was used for estimating the genome size of five brackishwater finfish and four shrimp species. The genome size for Lutjanus argentimaculatus was 0.95 ± 0.10 and 0.79 ± 0.01 pg for Scatophagus argus. The genome sizes for Chanos chanos (0.72 ± 0.01 pg), Etroplus suratensis (1.71 ± 0.16 pg) and Liza macrolepis (0.87 ± 0.02 pg) which are important aquaculture species are reported for the first time in this study. The phylogenetic tree constructed using sixty-seven sequence accessions of cytochrome c oxidase subunit 1 (COI) gene of Lates calcarifer revealed two separate clades. The Indian Lates calcarifer species with estimated genome size of 0.44 ± 0.02 pg belonged to a clade different than that of South East Asia and Australia reported to have larger genome size. The genome size for the four major species of genus Penaeus (Penaeus monodon, Penaeus indicus, Penaeus vannamei and Penaeus japonicus) were found in similar range. The genome size of female shrimps ranged from 2.91 ± 0.03 pg (P. monodon) to 2.14 ± 0.02 pg (P. japonicus). In male shrimps, the genome size ranged from 2.86 ± 0.06 pg (P. monodon) to 2.19 ± 0.02 pg (P. indicus). Significant difference was observed in the genome size between male and female shrimp of all species except in P. monodon. The highest relative difference of 12.78% was observed in the genome size between the either sex in P. indicus. The interspecific relative difference of 30.59% in genome size was highest between the male shrimps of P. monodon and P. indicus and 35.98% between the female shrimps of P. monodon and P. japonicus. The stored gills and pleopod tissues could be successfully used up to 3 weeks to estimate the genome size in shrimps.

MicroRNA in teleost fish

MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.

The kisspeptin system genes in teleost fish, their structure and regulation, with particular attention to the situation in Pleuronectiformes

It is well established that Kisspeptin regulates the onset of puberty in vertebrates through stimulation of the secretion of gonadotropin-releasing hormones. However, the function of kisspeptin in peripheral tissues and in other functions is still poorly understood. Recently, the evolution and distribution of kisspeptin genes in vertebrates has been clarified. In contrast to placental mammals, which have a single gene for the ligand (Kiss) and for the receptor (Kissr), fish may have up to three Kiss genes and up to four Kissr genes because of genome duplications. However, information on the genomic structure of the piscine kiss and kissr genes is still scarce. Furthermore, when data from several species is taken together, interspecific differences in the expression of kiss and kissr during the reproductive cycle are found. Here, we discuss data gathered from several fish species, but mainly from two flatfishes, the Senegalese sole and the Atlantic halibut, to address general questions on kiss gene structure, regulation and function. Flatfish are among the most derived fish species and the two species referred to above have only one ligand and one receptor, probably because of the genome reduction observed in Pleuronectiformes. However, gene analysis shows that both species have an alternative splicing mechanism based on intron retention, but the functions of the alternative isoforms are unclear. In the Senegalese sole, sex-related differences in the temporal and spatial expression of kiss and kissr were observed during a whole reproductive cycle. In addition, recent studies suggested that kisspeptin system gene expression is correlated to energy balance and reproduction. This suggests that kisspeptin signaling may involve different sources of information to synchronize important biological functions in vertebrates, including reproduction. We propose a set of criteria to facilitate the comparison of kiss and kissr gene expression data across species.

A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci

Tetraodontiform fishes represent one of the most peculiar radiations of teleost fishes. In spite of this, we do not currently have a consensus on the phylogenetic relationships among the major tetraodontiform lineages, with different morphological and molecular datasets all supporting contrasting relationships. In this paper we present the results of the analysis of tetraodontiform interrelationships based on two mitochondrial and 20 nuclear loci for 40 species of tetraodontiforms (representing all of the 10 currently recognized families), as well as three outgroups. Bayesian and maximum likelihood analyses of the concatenated dataset (18,682 nucleotides) strongly support novel relationships among the major tetraodontiform lineages. Our results recover two large clades already found in mitogenomic analyses (although the position of triacanthids differ), while they strongly conflict with hypotheses of tetraodontiform relationships inferred by previous studies based on morphology, as well as studies of higher-level teleost relationships based on nuclear loci, which included multiple tetraodontiform lineages. A parsimony gene-tree, species-tree analysis recovers relationships that are mostly congruent with the analyses of the concatenated dataset, with the significant exception of the position of the pufferfishes+porcupine fishes clade. Our findings suggest that while the phylogenetic placement of some tetraodontiform lineages (triacanthids, molids) remains problematic even after sequencing 22 loci, an overall molecular consensus is beginning to emerge regarding the existence of several major clades. This new hypothesis will require a re-evaluation of the phylogenetic usefulness of several morphological features, such as the fusion of several jaw bones into a parrot-like beak, or the reduction and loss of some of the fins, which may have occurred independently more times than previously thought.

Flow cytometric determination of genome size for eight commercially important fish species in China

The genome size (C value) of eight commercially important fish species in China was measured using flow cytometry. Chicken (Gallus domesticus) erythrocytes were used as reference cells. When using propidium iodide (PI) as the fluorescent dye, genome sizes were 1.09 ± 0.08, 2.75 ± 0.12, 1.05 ± 0.05, 1.35 ± 0.11, 0.99 ± 0.05, 0.90 ± 0.08, 0.90 ± 0.07, and 0.88 ± 0.07 pg for Japanese eel (Anguilla japonica), mullet (Myxocyprinus asiaticus), yellowcheek carp (Elopichthys bambusa), blunt snout bream (Megalobrama amblycephala), yellow catfish (Pelteobagrus fulvidraco), ricefield eel (Monopterus albus), mandarin fish (Siniperca chuatsi), and snakehead (Ophicephalus argus), respectively. However, genome sizes were 1.25 ± 0.00, 3.08 ± 0.02, 1.25 ± 0.00, 1.57 ± 0.01, 0.96 ± 0.01, 1.00 ± 0.01, 0.91 ± 0.01, and 0.89 ± 0.01 pg for these fishes, respectively, when 4', 6-diamidino-2-phenylindole (DAPI) was used as the fluorescent dye. Regardless of the dye used, the more evolutionarily advanced species had a smaller genome size than those with a lower evolutionary status. For each species, we also measured the size of erythrocytes and their nucleus and evaluated the relationships between erythrocyte size, nucleus size, chromosome number, and genome size. Genome size was positively correlated with erythrocyte nucleus size and chromosome number when using PI as the fluorescent dye, but it was only correlated with erythrocyte nucleus size when DAPI was used.

Replacing the first-generation dentition in pufferfish with a unique beak

Teleost fishes comprise approximately half of all living vertebrates. The extreme range of diversity in teleosts is remarkable, especially, extensive morphological variation in their jaws and dentition. Some of the most unusual dentitions are found among members of the highly derived teleost order Tetraodontiformes, which includes triggerfishes, boxfishes, ocean sunfishes, and pufferfishes. Adult pufferfishes (Tetraodontidae) exhibit a distinctive parrot-like beaked jaw, forming a cutting edge, unlike in any other group of teleosts. Here we show that despite novelty in the structure and development of this "beak," it is initiated by formation of separate first-generation teeth that line the embryonic pufferfish jaw, with timing of development and gene expression patterns conserved from the last common ancestor of osteichthyans. Most of these first-generation larval teeth are lost in development. Continuous tooth replacement proceeds in only four parasymphyseal teeth, as sequentially stacked, multigenerational, jaw-length dentine bands, before development of the functional beak. These data suggest that dental novelties, such as the pufferfish beak, can develop later in ontogeny through modified continuous tooth addition and replacement. We conclude that even highly derived morphological structures like the pufferfish beak form via a conserved developmental bauplan capable of modification during ontogeny by subtle respecification of the developmental module.

Comparative cytogenetics and heterochromatic patterns in two species of the genus Acanthostracion (Ostraciidae: Tetraodontiformes)

Some groups of fish, such as those belonging to the Order Tetraodontiformes, may differ significantly in the amount and location of heterochromatin in the chromosomes. There is a marked variation in DNA content of more than seven-fold among the families of this Order. However, the karyoevolutionary mechanisms responsible for this variation are essentially unknown. The largest genomic contents are present in species of the family Ostraciidae (2.20-2.60pg). The present study cytogenetically characterized two species of the family Ostraciidae, Acanthostracion polygonius and A. quadricornis, using conventional staining, C-bandings, Ag-NOR, CMA(3)/DAPI, AluI, PstI, EcoRI, TaqI and HinfI restriction enzymes (REs) and double FISH with 18S and 5S rDNA probes. The karyotypes of both species showed 2n=52 acrocentric chromosomes (FN=52; chromosome arms) and pronounced conserved structural characteristics. A significant heterochromatic content was observed equilocally distributed in pericentromeric position in all the chromosome pairs. This condition is unusual in relation to the karyotypes of other families of Tetraodontiformes and probability is the cause of the higher DNA content in Ostraciidae. Given the role played by repetitive sequences in the genomic reorganization of this Order, it is suggested that the conspicuous heterochromatic blocks, present in the same chromosomal position and with apparently similar composition, may have arisen or undergo evolutionary changes in concert providing clues about the chromosomal mechanisms which led to extensive variation in genomic content of different Tetraodontiformes families.

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.

Cytogenetic characterization of three Balistoidea fish species from the Atlantic with inferences on chromosomal evolution in the families Monacanthidae and Balistidae

The Tetraodontiformes are the most derived group of teleostean fish. Among other apomorphies, they are characterized by a high degree of fusions or significant bone loss in the head and body. In the early phylogenetic proposals presented for this order, the families Balistidae and Monacanthidae have been unanimously considered to be closely related. Although they have moderate species diversity, they are scarcely known in cytogenetic aspect and chromosomal pattern comparisons between these groups have yet to be established. The species Cantherhines macrocerus (Hollard,1853), Cantherhines pullus (Ranzani, 1842) (Monacanthidae) and Melichthys niger (Bloch, 1786) (Balistidae) were cytogenetically analyzed using conventional (Ag-impregnation, C-banding, CMA3- and DAPI-fluorescence) and molecular (FISH with an 18S rDNA probe) cytogenetic protocols. The karyotypes of all three species were very similar possessing diploid chromosome numbers 2n = 40 and composed exclusively of acrocentric chromosomes. Single NOR-bearing pair as well as positive heterochromatic blocks at pericentromeric regions were identified in the karyotypes of the three species studied. NOR-bearing sites were positively labeled after Ag-impregnation, C-banding, CMA3-fluorescence and FISH with an 18S rDNA probe but were negative after DAPI-fluorescence. Such remarkable shared conspicuous chromosomal characters corroborate either close phylogenetic relationship of these families, previously established by morphological and molecular data, or rather conservative nature of karyotype differentiation processes. The later hypothesis, however, appears less probable due to centric or in tandem fusions documented for another Balistoidea species.

Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

BACKGROUND

Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.

RESULTS

Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp).

CONCLUSION

Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish.

Genome size evaluation in Tetraodontiform fishes from the Neotropical region

Smooth pufferfish of the family Tetraodontidae had become pure genomic models because of the remarkable compaction of their genome. This trait seems to be the result of DNA loss following its divergence from the sister family Diodontidae, which possess larger genomes. In this study, flow cytometry was used for estimate the genome size of four pufferfish species from the Neotropical region. Cytogenetic data and confocal microscopy were also used attempting to confirm relationships between DNA content and cytological parameters. The haploid genome size was 0.71 + or - 0.03 pg for Sphoeroides greeleyi, 0.34 + or - 0.01 pg for Sphoeroides spengleri, 0.82 + or - 0.03 pg for Sphoeroides testudineus (all Tetraodontidae), and 1.00 + or - 0.03 pg for Chilomycterus spinosus (Diodontidae). These differences are not related with ploidy level, because 46 chromosomes are considered basal for both families. The value for S. spengleri represents the smallest vertebrate genome reported to date. Since erythrocyte cell and nuclear sizes are strongly correlated with genome size, the variation in this last is considered under both adaptive and evolutionary perspectives.

Cell size does not always correspond to genome size: phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution

At higher taxonomic levels, a significant correlation between genome size (GS) and erythrocyte size (ES) has been reported for many taxa. Under optimal DNA theories, several mechanisms presuming a causative link between GS and ES have been proposed to explain this seemingly general pattern. The correlation between GS and ES has been rarely tested among closely related organisms within an explicit phylogenetic framework. Eyelid geckos (family Eublepharidae) serve as a proper group to conduct such an analysis. We used flow cytometry to measure GS in 15 forms of eublepharids and conducted a phylogenetic reconstruction of GS and ES to test the successiveness of evolutionary shifts in these traits. Most parsimoniously, there were two independent increases and two decreases in GS during the evolution of eublepharids. Nevertheless, changes in GS and ES were not phylogenetically associated in a manner predicted by optimal DNA theories. Our results question the generality of causative bonds between DNA content and cell size and demonstrate that cell size cannot always serve as a proxy of GS. We suggest there is no need to expect a direct causative link between GS and ES to explain the correlation between GS and cell size at higher taxonomic levels. Such a correlation can be explained by simple mechanistic constraints and a combination of the population-genetic model of genome complexity with cell-size-metabolic rate relationship.

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity.

Evolution of genome size in fishes: a phylogenetic test of the Hinegardner and Rosen hypothesis

Despite remarkable advances in genomic studies over the past few decades, surprisingly little is known about the processes governing genome evolution at macroevolutionary timescales. In a seminal paper, Hinegardner and Rosen (Am Nat 106:621-644, 1972) suggested that taxa characterized by larger genomes should also display disproportionately stronger fluctuations in genome size. Therefore, according to the Hinegardner and Rosen (HR) hypothesis, there should be a negative correlation between average within-family genome size and its corresponding coefficient of variation (CV), a prediction that was supported by their analysis of the genomes of 275 species of fish. In this study we reevaluate the HR hypothesis using an expanded dataset (2050 genome size records). Moreover, in addition to the use of standard linear regression techniques, we also conducted modern comparative analyses that take into account phylogenetic non-independence. Our analyses failed to confirm the negative relationship detected in the original study, suggesting that the evolution of genome size in fishes might be more complex than envisioned by the HR hypothesis. Interestingly, the frequency distribution of fish genome sizes was strongly skewed, even on a logarithmic scale, suggesting that the dynamics underlying genome size evolution are driven by multiplicative phenomena, which might include chromosomal rearrangements and the expansion of transposable elements.

Physical mapping of 5S and 45S rDNA loci in pufferfishes (Tetraodontiformes)

Chromosomal features, location and variation of the major and minor rDNA genes cluster were studied in three pufferfish species: Sphoeroides greeleyi and Sphoeroides testudineus (Tetraodontidae) and Cyclichthys spinosus (Diodontidae). The location of the major rDNA was revealed with an 18S probe in two loci for all species. The minor rDNA loci (5S rDNA) was found in one chromosome pair in tetraodontid fishes and four sites located on two distinct chromosomal pairs in C. spinosus. A syntenical organization was not observed among the ribosomal genes. Signal homogeneity for GC/AT-DNA specific fluorochromes was observed in diodontid fish except in the NORs regions, which were CMA3-positive. Giemsa karyotypes of tetraodontid species presents 2n=46, having the same diploid value of other Sphoeroides species that have been investigated. On the other hand, the karyotype of C. spinosus, described for the first time, shows 2n=50 chromosomes (4m+18sm+12st+16a). The foreknowledge of the karyotypic structure of this group and also the physical mapping of certain genes could be very helpful for further DNA sequence analysis.

Cladogenetic correlates of genomic expansions in the recent evolution of actinopterygiian fishes

Genomic expansions via regional gene duplications and polyploidization events have been implicated as catalysts for rapid cladogenetic speciation in some fish taxa, but any general relationships between genome sizes and patterns of evolutionary radiation remain poorly characterized. Here we examine empirical correlations between genome size and species richness (number of extant species within a given clade) both across Actinopterygii (ray-finned fishes) and within several large actinopterygiian clades. We conducted the analyses both without and with correction (by independent contrasts) for phylogenetic effects. Across the full suite of 461 surveyed genera, relatively small but significant positive correlations were present between species richness and evolutionary increases in C-value. Although many variables (including ecological and behavioural factors) clearly can influence speciation rates, the current results are consistent with the notion that genomic architecture may play a role in species proliferation as well.

Myogenin in model pufferfish species: Comparative genomic analysis and thermal plasticity of expression during early development

Myogenin (Myog) is a muscle-specific basic helix-loop-helix transcription factor that plays an essential role in the specification and differentiation of myoblasts. The myogenin genes from the tiger pufferfish, Takifugu rubripes, and green-spotted pufferfish, Tetraodon nigroviridis, were cloned and a comparative genomic analysis performed. The gene encoding myogenin is composed of three exons and has a relatively similar genomic structure in T. rubripes, T. nigroviridis and human. Introns 1 and 2 were approximately 2-fold and 8-fold longer respectively in human than pufferfish. Myogenin is located in a 100 kb region of conserved synteny between these organisms, corresponding to chromosome 1 in human, chromosome 11 in T. nigroviridis and scaffold 208 in T. rubripes. Pufferfish myogenin contained a serine-rich region at the carboxyl terminus that is highly conserved amongst teleosts. During embryonic development of T. rubripes, myogenin was expressed in a rostral-caudal gradient in the developing somites and subsequently during the pharyngula period in the pectoral fin bud primordia, jaw muscles and extraocular muscle precursors. In T. rubripes, the time required to form a somite pair during the linear phase of somitogenesis ( identical withsomite-interval) was 122 min, 97 min and 50 min in embryos incubated at 15, 18 and 21 degrees C, respectively. Myogenin mRNA transcripts were quantified using qPCR and normalised to the highest level of expression. Peak myogenin expression occurred later with respect to developmental stage (standardised using somite-intervals) and was over 2-fold higher at 21 degrees C than at either 18 or 15 degrees C. Changes in the relative timing and intensity of myogenin expression are a potential mechanism for explaining thermal plasticity of muscle phenotype in larvae via effects on the differentiation programme.

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes

Nuclear inserted copies of mitochondrial origin (numts) vary widely among eukaryotes, with human and plant genomes harboring the largest repertoires. Numts were previously thought to be absent from fish species, but the recent release of three fish nuclear genome sequences provides the resource to obtain a more comprehensive insight into the extent of mtDNA transfer in fishes. From the sequence analyses of the genomes of Fugu rubripes, Tetraodon nigroviridis, and Danio rerio, we have identified 2, 5, and 10 recent numt integrations, respectively, which integrated into those genomes less than 0.6 million years (Myr) ago. Such results contradict the hypothesis of absence or rarity of numts in fishes, as (i) the ratio of numts to the total size of the nuclear genome in T. nigroviridis was superior to the ratio observed in several higher vertebrate species (e.g., chicken, mouse, and rat), and only surpassed by humans, and (ii) the mtDNA coverage transferred to the nuclear genome of D. rerio is exceeded only by human and mouse, within the whole range of eukaryotic genomes surveyed for numts. Additionally, 335, 336, and 471 old numts (>12.5 Myr) were detected in F. rubripes, T. nigroviridis, and D. rerio, respectively. Surprisingly, old numts are inserted preferentially into known or predicted genes, as inferred for recent numts in human. However, because in fish genomes such integrations are old, they are likely to represent evolutionary successes and they may be considered a potential important evolutionary mechanism for the enhancement of genomic coding regions.

Genome Size Evolution in New Zealand Triplefin Fishes

The genome sizes of 18 species of New Zealand triplefin fishes (family Tripterygiidae) were determined by flow cytometry of erythrocytes. The evolutionary relationships of these species were examined with a molecular phylogeny derived from DNA sequence data based on 1771 base pairs from fragments of three mitochondrial loci (12S and 16S ribosomal RNA, and the control region) and one nuclear locus (ETS2). Haploid genome sizes ranged from .85 pg (1C) to 1.28 pg with a mean of 1.15 +/- .01pg. Genome size appeared to be highly plastic, with up to 20% variation occurring within genera and a 50% difference in size between the smallest and the largest genome. No evidence was found to indicate polyploidy as a mechanism for speciation in New Zealand triplefins. Factors suggested to influence genome sizes of other organisms, such as morphological complexity, neoteny, and longevity, do not appear to be associated with shifts in the genome sizes of New Zealand triplefins.

Evolution and diversity of fish genomes

The ray-finned fishes ('fishes') vary widely in genome size, morphology and adaptations. Teleosts, which comprise approximately 23600 species, constitute >99% of living fishes. The radiation of teleosts has been attributed to a genome duplication event, which is proposed to have occurred in an ancient teleost. But more evidence is required to support the genome-duplication hypothesis and to establish a causal relationship between additional genes and teleost diversity. Fish genomes seem to be 'plastic' in comparison with other vertebrate genomes because genetic changes, such as polyploidization, gene duplications, gain of spliceosomal introns and speciation, are more frequent in fishes.

Insertion-deletion biases and the evolution of genome size

Numerous theories have been proposed to account for the pronounced differences in the quantity of non-coding DNA among eukaryotic genomes, but the current repertoire remains incomplete because the only explicit mechanisms it provides involve DNA gain. It has been proposed more recently that biases in spontaneous insertions and deletions (indels) can lead to genome shrinkage by mutational mechanisms alone. The present article provides the first detailed critical discussion of this approach, and covers three different ideas related to it: (1) the general notion of DNA loss by deletion bias, (2) the "DNA loss hypothesis" which supposes that variation in genome size can be attributed to differences in DNA loss rate, and (3) the "mutational equilibrium model" which attempts to describe the long-term evolution of genome size. The mutational equilibrium model is found to be problematic, and it is noted that DNA loss by small indels is too slow in real time to determine variation in genome size above a relatively low threshold. Some alternative explanations for the observed patterns are provided, and the critique also identifies some potential problems with the current dataset. These include a failure to cite a more detailed (and somewhat contradictory) mammalian dataset, a questionable use of arithmetic means with highly skewed data, and important discrepancies among the particular DNA sequences so far analyzed. Overall, evolutionary reductions in genome size are considered important, but the specific mechanism relating to small deletion bias is far too weak to be accepted as a primary determinant of genome size variation in general.

Real-time PCR-based method for the estimation of genome sizes

The fast and reliable estimation of the genome sizes of various species would allow for a systematic analysis of many organisms and could reveal insights into evolutionary processes. Many methods for the estimation of genome sizes have already been described. The classical methods are based on the determination of the phosphate content in the DNA backbone of total DNA isolated from a defined number of cells or on reassociation kinetics of high molecular weight genomic DNA (c(0)t assay). More recent techniques employ DNA-specific fluorescent dyes in flow cytometry analysis, image analysis or absorption cytometry after Feulgen staining. The method presented here is based on the absolute quantification of genetic elements in a known amount (mass) of genomic DNA by real-time quantitative PCR. The method was evaluated on three different eukaryotic species, Saccharomyces cerevisiae (12.1 Mb), Xiphophorus maculatus (550 Mb) and Homo sapiens sapiens (2.9 Gb), and found to be fast, highly accurate and reliable.

Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes

Smooth pufferfish of the family Tetraodontidae have the smallest vertebrate genomes yet measured. They have a haploid genome size of approximately 400 million bp (Mb), which is almost eight times smaller than the human genome. Given that spiny pufferfish from the sister family Diodontidae and a fish from the outgroup Molidae have genomes twice as large as smooth puffers, it appears that the genome size of smooth puffers has contracted in the last 50-70 million years since their divergence from the spiny puffers. Here we use renaturation kinetics to compare the repetitive nature of the smooth and spiny puffer genomes. We also estimate the rates of small (<400 bp) insertions and deletions in smooth and spiny puffers using defunct non-LTR retrotransposons. We find a significantly greater abundance of a transposon-like repetitive DNA class in spiny puffers relative to smooth puffers, in addition to nearly identical indel rates. We comment on the role that large insertions may play in the evolution of genome size in these two groups.