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

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history

The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.

High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes

This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes.

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.

PiggyBac Transposon Mining in the Small Genomes of Animals

TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.

Comparative genomics reveals insights into anuran genome size evolution

BACKGROUND

Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.

RESULTS

Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.

CONCLUSIONS

Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.

Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera)

BACKGROUND

Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS).

RESULTS

Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)_n, (AC)_n, (CAA)_n, (AAAC)_n, (AACAA)_n and (AAACAA)_n, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)_n, (AC)_n, (TAT)_n, (TTTA)_n, (AACAA)_n and (GAGAGG)_n, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution.

CONCLUSIONS

Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.

New insights into the evolutionary dynamic and lineage divergence of gasdermin E in metazoa

Gasdermin (GSDM) is a family of pore-forming proteins that induce pyroptosis. To date, the origin and evolution of GSDM in Metazoa remain elusive. Here, we found that GSDM emerged early in Placozoa but is absent in a large number of invertebrates. In the lower vertebrate, fish, three types of GSDME, i.e., GSDMEa, GSDMEb, and a previously unreported type (designated GSDMEc), were idenitied. Evolutionarily, the three GSDMEs are distinctly separated: GSDMEa is closely related to tetrapod GSDME; GSDMEb exists exclusively in fish; GSDMEc forms the lineage root of tetrapod GSDMA/B/C/D. GSDMEc shares conserved genomic features with and is probably the prototype of GSDMA, which we found existing in all tetrapod classes. GSDMEc displays fast evolutionary dynamics, likely as a result of genomic transposition. A cross-metazoan analysis of GSDME revealed that GSDMEa shares a conserved caspase recognition motif with the GSDME of tetrapods and cnidarians, whereas GSDMEb has a unique caspase recognition motif similar to that of mammalian GSDMD, and GSDMEc exhibits no apparent caspase recognition motif. Through functional test, four highly conserved residues in vertebrate GSDME proved to be essential to auto-inhibition. Together our results provide new insights into the origin, evolution, and function of metazoan GSDMs.

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.

Genome-wide oscillations in G + C density and sequence conservation

Eukaryotic genomes typically show a uniform G + C content among chromosomes, but on smaller scales, many species have a G + C density that fluctuates with a characteristic wavelength. This oscillation is evident in many insect species, with wavelengths ranging between 700 bp and 4 kb. Measures of evolutionary conservation oscillate in phase with G + C content, with conserved regions having higher G + C. Loci with large regulatory regions show more regular oscillations; coding sequences and heterochromatic regions show little or no oscillation. There is little oscillation in vertebrate genomes in regions with densely distributed mobile repetitive elements. However, species with few repeats show oscillation in both G + C density and sequence conservation. These oscillations may reflect optimal spacing of cis-regulatory elements.

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum

The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.

Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

BACKGROUND

Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected.

RESULTS

The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. non-repetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome.

CONCLUSION

Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation.

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

Identification of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis

Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G aculeatus.

The first complete genomes of Metalmarks and the classification of butterfly families

Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, respectively, they become the largest available Lepidoptera genomes. Comparison of butterfly genomes shows that the divergence between Riodinidae and Lycaenidae dates to the time when other families started to diverge into subfamilies. Thus, Riodinidae may be considered a subfamily of Lycaenidae. Calephelis species exhibit unique gene expansions in actin-disassembling factor, cofilin, and chitinase. The functional implications of these gene expansions are not clear, but they may aid molting of caterpillars covered in extensive setae. The two Calephelis species diverged about 5 million years ago and they differ in proteins involved in metabolism, circadian clock, regulation of development, and immune responses.

Dynamics of genome size evolution in birds and mammals

Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

The contribution of transposable elements to size variations between four teleost genomes

Background

Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained.

Results

In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome.

Conclusion

Overall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.

Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.-Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400-800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.

Chromosome evolution in fishes: a new challenging proposal from Neotropical species

We present a database containing cytogenetic data of Neotropical actinopterygian fishes from Venezuela obtained in a single laboratory for the first time. The results of this study include 103 species belonging to 74 genera assigned to 45 families and 17 out of the 40 teleost orders. In the group of marine fishes, the modal diploid number was 2n=48 represented in 60% of the studied species, while in the freshwater fish group the modal diploid complement was 2n=54, represented in 21.21 % of the studied species. The average number of chromosomes and the mean FN were statistically higher in freshwater fish than in marine fish. The degree of diversification and karyotype variation was also higher in freshwater fish in contrast to a more conserved cytogenetic pattern in marine fish. In contrast to the assumption according to which 48 acrocentric chromosomes was basal chromosome number in fish, data here presented show that there is an obvious trend towards the reduction of the diploid number of chromosomes from values near 2n=60 with high number of biarmed chromosomes in more basal species to 2n=48 acrocentric elements in more derived Actinopterygii.

Patterns of genome size diversity in bats (order Chiroptera)

Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").

The correlation of genome size and DNA methylation rate in metazoans

Total DNA methylation rates are well known to vary widely between different metazoans. The phylogenetic distribution of this variation, however, has not been investigated systematically. We combine here publicly available data on methylcytosine content with the analysis of nucleotide compositions of genomes and transcriptomes of 78 metazoan species to trace the evolution of abundance and distribution of DNA methylation. The depletion of CpG and the associated enrichment of TpG and CpA dinucleotides are used to infer the intensity and localization of germline CpG methylation and to estimate its evolutionary dynamics. We observe a positive correlation of the relative methylation of CpG motifs with genome size. We tested this trend successfully by measuring total DNA methylation with LC/MS in orthopteran insects with very different genome sizes: house crickets, migratory locusts and meadow grasshoppers. We hypothesize that the observed correlation between methylation rate and genome size is due to a dependence of both variables from long-term effective population size and is driven by the accumulation of repetitive sequences that are typically methylated during periods of small population sizes. This process may result in generally methylated, large genomes such as those of jawed vertebrates. In this case, the emergence of a novel demethylation pathway and of novel reader proteins for methylcytosine may have enabled the usage of cytosine methylation for promoter-based gene regulation. On the other hand, persistently large populations may lead to a compression of the genome and to the loss of the DNA methylation machinery, as observed, e.g., in nematodes.

Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage

We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics. We identify that the zebrafish, Danio rerio, has an unusual distribution of intron sizes, with a greater number of larger introns in general and a notable peak in the frequency of introns of approximately 500 to 2,000 bp compared with the monotonically decreasing frequency distributions of the other fish. We determine that 47% of D. rerio introns are composed of repetitive sequences, although the remainder, over 331 Mb, is not. Because repetitive elements may be the origin of the majority of all noncoding DNA, it is likely that the remaining D. rerio intronic sequence has an ancient repetitive origin and has since accumulated so many mutations that it can no longer be recognized as such. To study such an ancient expansion of repeats in the Danio, lineage will require further comparative analysis of fish genomes incorporating a broader distribution of teleost lineages.

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.

Molecular evolution of Na+ channels in teleost fishes

Voltage-dependent sodium channels are critical for electrical excitability. Invertebrates possess a single sodium channel gene; two rounds of genome duplication early in vertebrates increased the number to four. Since the teleost-tetrapod split, independent gene duplications in each lineage have further increased the number of sodium channel genes to 10 in tetrapods and 8 in teleosts. Here we review how the occurrence of multiple sodium channel paralogs has influenced the evolutionary history of three groups of fishes: pufferfish, gymnotiform and mormyriform electric fish. Pufferfish (tetraodontidae) produce a neurotoxin, tetrodotoxin, that binds to and blocks the pore of sodium channels. Pufferfish evolved resistance to their own toxins by amino acid substitutions in the pore of their sodium channels. These substitutions had to occur in parallel across multiple paralogs for organismal resistance to evolve. Gymnotiform and mormyriform fishes independently evolved electric organs to generate electricity for communication and object localization. Two sodium channel genes are expressed in muscle in most fishes. In both groups of weakly electric fishes, one gene lost its expression in muscle and became compartmentalized in the evolutionary novel electric organ, which is a muscle derivative. This gene then evolved at elevated rates, whereas the gene that is still expressed in muscle does not show elevated rates of evolution. In the electric organ-expressing gene, amino acid substitutions occur in parts of the channel involved in determining how long the channel will be open or closed. The enhanced rate of sequence evolution of this gene likely underlies the species-level variations in the electric signal.

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.

Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers

The clustering of transcription factor binding sites in developmental enhancers and the apparent preferential conservation of clustered sites have been widely interpreted as proof that spatially constrained physical interactions between transcription factors are required for regulatory function. However, we show here that selection on the composition of enhancers alone, and not their internal structure, leads to the accumulation of clustered sites with evolutionary dynamics that suggest they are preferentially conserved. We simulated the evolution of idealized enhancers from Drosophila melanogaster constrained to contain only a minimum number of binding sites for one or more factors. Under this constraint, mutations that destroy an existing binding site are tolerated only if a compensating site has emerged elsewhere in the enhancer. Overlapping sites, such as those frequently observed for the activator Bicoid and repressor Krüppel, had significantly longer evolutionary half-lives than isolated sites for the same factors. This leads to a substantially higher density of overlapping sites than expected by chance and the appearance that such sites are preferentially conserved. Because D. melanogaster (like many other species) has a bias for deletions over insertions, sites tended to become closer together over time, leading to an overall clustering of sites in the absence of any selection for clustered sites. Since this effect is strongest for the oldest sites, clustered sites also incorrectly appear to be preferentially conserved. Following speciation, sites tend to be closer together in all descendent species than in their common ancestors, violating the common assumption that shared features of species' genomes reflect their ancestral state. Finally, we show that selection on binding site composition alone recapitulates the observed number of overlapping and closely neighboring sites in real D. melanogaster enhancers. Thus, this study calls into question the common practice of inferring "cis-regulatory grammars" from the organization and evolutionary dynamics of developmental enhancers.

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.

Evolution of teleost fish retroviruses: characterization of new retroviruses with cellular genes

The interactions between retroviruses and their hosts can be of a beneficial or detrimental nature. Some endogenous retroviruses are involved in development, while others cause disease. The Genome Parsing Suite (GPS) is a software tool to track and trace all Retroid agents in any sequenced genome (M. A. McClure et al., Genomics 85:512-523, 2005). Using the GPS, the retroviral content was assessed in four model teleost fish. Eleven new species of fish retroviruses are identified and characterized. The reverse transcriptase protein sequences were used to reconstruct a fish retrovirus phylogeny, thereby, significantly expanding the epsilon-retrovirus family. Most of these novel retroviruses encode additional genes, some of which are homologous to cellular genes that would confer viral advantage. Although the fish divergence is much more ancient, retroviruses began infecting fish genomes approximately 4 million years ago.

Genomic insights into marine microalgae

Marine eukaryotic photosynthesis is dominated by a diverse group of unicellular organisms collectively called microalgae. Microalgae include cells derived from a primary endosymbiotic event (similar to land plants) and cells derived from subsequent secondary and/or tertiary endosymbiotic events. These latter cells are chimeras of several genomes and dominate primary production in the marine environment. Two consequences of multiple endosymbiotic events include complex targeting mechanisms to allow nuclear-encoded proteins to be imported into the plastid and coordination of enzymes, potentially from disparate originator cells, to form complete metabolic pathways. In this review, we discuss the forces that shaped the genomes of marine microalgae and then discuss some of the metabolic consequences of such a complex evolutionary history. We focus our metabolic discussion on carbon, nitrogen, and iron. We then discuss biomineralization and new evidence for programmed cell death in microalgae. We conclude with a short summary on advances in genetic manipulation of microalgae and thoughts on the future directions of marine algal genomics.

Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family

Approximately 75% of vertebrate proteins belong to protein families encoded by multiple evolutionarily related genes, a pattern that emerged as a result of gene and genome duplications over the course of vertebrate evolution. In families of genes with similar or related functions, adaptation to a strong selective agent should involve multiple adaptive changes across the entire gene family. However, we know of no evolutionary studies that have explicitly addressed this point. Here, we show how 4 taxonomically diverse species of pufferfishes (Tetraodontidae) each evolved resistance to the guanidinium toxins tetrodotoxin (TTX) and saxitoxin (STX) via parallel amino acid replacements across all 8 sodium channels present in teleost fish genomes. This resulted in diverse suites of coexisting sodium channel types that all confer varying degrees of toxin resistance, yet show remarkable convergence among genes and phylogenetically diverse species. Using site-directed mutagenesis and expression of a vertebrate sodium channel, we also demonstrate that resistance to TTX/STX is enhanced up to 15-fold by single, frequently observed replacements at 2 sites that have not previously been implicated in toxin binding but show similar or identical replacements in pufferfishes and in distantly related vertebrate and nonvertebrate animals. This study presents an example of natural selection acting upon a complete gene family, repeatedly arriving at a diverse but limited number of adaptive changes within the same genome. To be maximally informative, we suggest that future studies of molecular adaptation should consider all functionally similar paralogs of the affected gene family.

Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis

Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G. aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G. aculeatus.

Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster

LTR and non-LTR retrotransposons exhibit distinct patterns of abundance within the Drosophila melanogaster genome, yet the causes of these differences remain unknown. Here we investigate whether genomic differences between LTR and non-LTR retrotransposons reflect systematic differences in their insertion history. We find that for 17 LTR and 10 non-LTR retrotransposon families that evolve under a pseudogene-like mode of evolution, most elements from LTR families have integrated in the very recent past since colonization of non-African habitats ( approximately 16,000 years ago), whereas elements from non-LTR families have been accumulating in overlapping waves since the divergence of D. melanogaster from its sister species, Drosophila simulans ( approximately 5.4 Mya). LTR elements are significantly younger than non-LTR elements, individually and by family, in regions of high and low recombination, and in genic and intergenic regions. We show that analysis of transposable element (TE) nesting provides a method to calculate transposition rates from genome sequences, which we estimate to be one to two orders of magnitude lower than those that are based on mutation accumulation studies. Recent LTR integration provides a nonequilibrium alternative for the low population frequency of LTR elements in this species, a pattern that is classically interpreted as evidence for selection against the transpositional increase of TEs. Our results call for a new class of population genetic models that incorporate TE copy number, allele frequency, and the age of insertions to provide more powerful and robust inferences about the forces that control the evolution of TEs in natural populations.

The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates

It is increasingly recognized that insertions and deletions (indels) are an important source of genetic as well as phenotypic divergence and diversity. We analyzed length polymorphisms identified through partial (0.25x) shotgun sequencing of three breeds of domestic chicken made by the International Chicken Polymorphism Map Consortium. A data set of 140,484 short indel polymorphisms in unique DNA was identified after filtering for microsatellite structures. There was a significant excess of tandem duplicates at indel sites, with deletions of a duplicate motif outnumbering the generation of duplicates through insertion. Indel density was lower in microchromosomes than in macrochromosomes, in the Z chromosome than in autosomes, and in 100 bp of upstream sequence, 5'-UTR, and first introns than in intergenic DNA and in other introns. Indel density was highly correlated with single nucleotide polymorphism (SNP) density. The mean density of indels in pairwise sequence comparisons was 1.9 x 10(-4) indel events/bp, approximately 5% the density of SNPs segregating in the chicken genome. The great majority of indels involved a limited number of nucleotides (median 1 bp), with A-rich motifs being overrepresented at indel sites. The overrepresentation of deletions at tandem duplicates indicates that replication slippage in duplicate sequences is a common mechanism behind indel mutation. The correlation between indel and SNP density indicates common effects of mutation and/or selection on the occurrence of indels and point mutations.

Phylogenetic relationships and gene expression pattern of three different cathepsin L (Ctsl) isoforms in zebrafish: Ctsla is the putative yolk processing enzyme

Certain cysteine proteases, such as cathepsin L (Ctsl), have been involved in yolk processing mechanisms in oocytes and embryos of lower vertebrates. In zebrafish (Danio rerio), three different ctsl genes, ctsla, ctslb and ctslc, have been found in the genome, but their pattern of expression, as well as information on which the encoded enzymes are potentially involved in yolk absorption during embryogenesis, is unknown. Here, phylogenetic and gene structure analysis revealed that zebrafish ctsla and ctslb genes are similar, showing a highly conserved structure in comparison with human ctsl, while ctslc presents different exon organization together with an earlier evolution. Thus, ctslc appears to be evolved from a common ancestral ctsl-like gene, possibly through an early duplication event, whereas ctsla and ctslb may be originated from a second duplication mechanism. Zebrafish ctsla, ctslb and ctslc also showed different patterns of mRNA expression during embryogenesis and in adult tissues. While Ctsla transcripts were accumulated in embryos throughout development and in the adult ovary, those encoding Ctslb were detected only in embryos around the time of hatching as previously reported, and those for Ctslc appeared only in larvae and in some adult tissues, but not in the ovary. In zebrafish and killifish (Fundulus heteroclitus) embryos, Ctsla mRNA was first detected in blastomers, and later in development it was localized in cells of the yolk syncytial layer, an embryonic structure involved in yolk absorption. These data therefore suggested that Ctsla is most likely the putative protease involved in yolk processing in fish embryos, while Ctslc seems not to be required during early embryogenesis in zebrafish.

The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

Evolution of the genome size in eukaryotes is often affected by changes in the noncoding sequences, for which insertions and deletions (indels) of small nucleotide sequences and amplification of repetitive elements are considered responsible. In this study, we compared the genomic DNA sequences of two kinds of fish, medaka (Oryzias latipes) and fugu (Takifugu rubripes), which show two-fold difference in the genome size (800 Mb vs. 400 Mb). We selected a contiguous DNA sequence of 790 kb from the medaka chromosome LG22 (linkage group 22), and made a precise comparison with the sequence (387 kb) of the corresponding region of Takifugu. The sequence of 178 kb in total was aligned common between two fishes, and the remaining sequences (612 kb for medaka and 209 kb for fugu) were found abundant in various repetitive elements including many types of unclassified low copy repeats, all of which accounted for more than a half (54%) of the genome size difference. Furthermore, we identified a significant difference in the length ratio of the unaligned sequences that locate between the aligned sequences (USBAS), particularly after eliminating known repetitive elements. These USBAS with no repetitive elements (USBAS-nr) located within the intron and intergenic region. These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size.

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales - a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R (2) = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.

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.

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

Background

Several lines of evidence suggest that codon usage in the Drosophila saltans and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages.

Results and discussion

To gain additional insight into this question, we quantified background substitutional patterns in the saltans/willistoni group using inactive copies of a novel, Q-like retrotransposable element. We demonstrate that the pattern of background substitutions in the saltans/willistoni lineage has shifted to a significant degree, primarily due to changes in mutational biases. These differences predict a lower equilibrium GC content in the genomes of the saltans/willistoni species compared with that in the D. melanogaster species group. The magnitude of the difference can readily account for changes in intronic GC content, but it appears insufficient to explain changes in codon usage within the saltans/willistoni lineage.

Conclusion

We suggest that the observed changes in codon usage in the saltans/willistoni clade reflects either lineage-specific changes in the definitions of preferred and unpreferred codons, or a weaker selective pressure on codon bias in this lineage.

The genome ofOscheius tipulae: determination of size, complexity, and structure by DNA reassociation using fluorescent dye

This work describes the physicochemical characterization of the genome and telomere structure from the nematode Oscheius tipulae CEW1. Oscheius tipulae is a free-living nematode belonging to the family Rhabditidae and has been used as a model system for comparative genetic studies. A new protocol that combines fluorescent detection of double-stranded DNA and S1 nuclease was used to determine the genome size of O. tipulae as 100.8 Mb (approximately 0.1 pg DNA/haploid nucleus). The genome of this nematode is made up of 83.4% unique copy sequences, 9.4% intermediate repetitive sequences, and 7.2% highly repetitive sequences, suggesting that its structure is similar to those of other nematodes of the genus Caenorhabditis. We also showed that O. tipulae has the same telomere repeats already found in Caenorhabditis elegans at the ends and in internal regions of the chromosomes. Using a cassette-ligation-mediated PCR protocol we were able to obtain 5 different putative subtelomeric sequences of O. tipulae, which show no similarity to C. elegans or C. briggsae subtelomeric regions. DAPI staining of hermaphrodite gonad cells show that, as detected in C. elegans and other rhabditids, O. tipulae have a haploid complement of 6 chromosomes.Key words: Oscheius tipulae, Caenorhabditis elegans, DNA reassociation, telomere, genome size, karyotype.

Fugu genome does not contain mitochondrial pseudogenes

Contrary to previous observations that fish genomes are devoid of nuclear mitochondrial pseudogenes, a genome-wide survey identified a large number of "recent" and "ancient" nuclear mitochondrial DNA fragments (Numts) in the whole-genome sequences of the fugu (Takifugu rubripes), Tetraodon nigroviridis, and zebrafish (Danio rerio). We have analyzed the latest assembly (v4.0) of the fugu genome and show that, like the Anopheles genome, the fugu nuclear genome does not contain mitochondrial pseudogenes. Fugu assembly v4.0 contains a single scaffold representing the near complete sequence of the fugu mitochondria. The "recent" Numts identified by the previous study in fugu assembly v2.0 are in fact shotgun sequences of mitochondrial DNA that were misassembled with the nuclear sequences, whereas the "ancient" Numts appear to be the result of spurious matches. It is likely that the Numts identified in the genomes of Tetraodon and zebrafish are also similar artifacts. Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification.

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.

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.

Evolution of genome size: multilevel selection, mutation bias or dynamical chaos?

In the past two years, new data on conceptual aspects of the evolution of eukaryotic genome size have appeared, including the adaptivity of genome enlargement, the mechanisms of genome size change and the relation of genome size to organismal complexity. New data on the hypotheses of "selfish DNA" and "mutational equilibrium" have been recently obtained. A relationship is emerging between the intragenomic distribution of noncoding DNA and differential gene expression, which suggests that noncoding DNA is involved in epigenetic organization of the genome and organismal complexity. The standpoint of dynamical chaos, which integrates multilevel selection and mutation biases, may provide a framework for studying the evolution of genome size.

What tangled web: barriers to rampant horizontal gene transfer

Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional "tree of life".(5-10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT.

Comparative genomics

The genomes from three mammals (human, mouse, and rat), two worms, and several yeasts have been sequenced, and more genomes will be completed in the near future for comparison with those of the major model organisms. Scientists have used various methods to align and compare the sequenced genomes to address critical issues in genome function and evolution. This review covers some of the major new insights about gene content, gene regulation, and the fraction of mammalian genomes that are under purifying selection and presumed functional. We review the evolutionary processes that shape genomes, with particular attention to variation in rates within genomes and along different lineages. Internet resources for accessing and analyzing the treasure trove of sequence alignments and annotations are reviewed, and we discuss critical problems to address in new bioinformatic developments in comparative genomics.

Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis

In this paper, we provide evidence for the body temperature effect on the formation of GC-rich isochores, by analysing genomic sequences from two puffer fishes living at different temperatures. The higher body temperature of Tetraodon nigroviridis compared to Takifugu rubripes (DeltaT approximately 15 degrees C) appears to be the cause of a higher compositional heterogeneity of the former due to the formation of GC-rich regions. Such an effect does not only concern large DNA segments but also coding sequences.

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.