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BackgroundTeleost fishes account for over half of extant vertebrate species. A core question in biology is how genomic changes drive phenotypic diversity that relates to the origin of teleost fishes.ResultsHere, we used comparative genomic analyses with chromosome assemblies of diverse lineages of vertebrates and reconstructed an ancestral vertebrate genome, which revealed phylogenomic trajectories in vertebrates. We found that the whole-genome-wide chromosome fission/fusions took place in theMonopterus albuslineage after the 3-round whole-genome duplication. Four times of genomic fission/fusions events resulted in the whole genome-wide chromosome fusions in the genomic history of the lineage. In addition, abundant recently evolved new genes for reproduction emerged in theMonopterus albusafter separated from medaka. Notably, we described evolutionary trajectories of conserved blocks related to sex determination genes in teleosts.ConclusionsThese data pave the way for a better understanding of genomic evolution in extant teleosts.

The factors that drive the rapid changes in abundance of tandem arrays of highly repetitive sequences, known as satellite DNA, are not well understood. Drosophila virilis has one of the highest relative amounts of simple satellites of any organism that has been studied, with an estimated >40% of its genome composed of a few related 7-bp satellites. Here, we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the highly abundant AAACTAC satellite family arose from a related satellite in the branch leading to the virilis phylad 4.5–11 Ma before exploding in abundance in some species of the clade. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. By analyzing multiple strains of D. virilis, we saw that the abundances of two centromere-proximal satellites are anticorrelated along a geographical gradient, which we suggest could be caused by ongoing conflicts at the centromere. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes including selection, meiotic drive, and constraints on satellite sequence and abundance.

Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small RNAs are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality. To test the functionality of intergenic inverted duplicates without known functions, we used mirror duplicates, a type of repetitive DNA motifs with few reported functions and little potential to form hairpins when transcribed, as a nonfunctional control. We identified large numbers of inverted duplicates within intergenic regions of human and mouse genomes, as well as 19 other vertebrate genomes. Structure characterization of these inverted duplicates revealed higher proportion to form stable hairpins compared with converted mirror duplicates, suggesting that inverted duplicates may produce hairpin RNAs. Expression profiling across tissues demonstrated that 7.8% of human and 5.7% of mouse inverted duplicates were expressed even under strict criteria. We found that expressed inverted duplicates were more likely to be structurally stable than both unexpressed inverted duplicates and expressed converted mirror duplicates. By dating inverted duplicates in the vertebrate phylogenetic tree, we observed higher conservation of inverted duplicates than mirror duplicates. These observations support the notion that expressed inverted duplicates may be functional through forming hairpin RNAs.

The factors that drive the rapid changes in satellite DNA genomic composition we see in eukaryotes are not well understood. Drosophila virilis has one of the highest relative amounts of simple satellites of any organism that has been studied, with an estimated 40+% of its genome composed of a few related 7 bp satellites. Here we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the satellite family arose in the branch leading to the virilis phylad 4.5 - 11 million years ago. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. The amount of satellite DNA is lowest in the species with the smallest effective population size in the D. virilis phylad, contrary to what would be expected if satellites were only evolving under weak negative selection. We found evidence for transposable elements flanking the satellite arrays as well as recent insertions into the arrays. By analyzing multiple strains of D. virilis, we saw that one centromere-proximal satellite is undergoing an expansion, while the other is contracting in a correlated manner, suggesting possible trade-offs or competition between satellites. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes like positive selection, meiotic drive, and constraints on satellite sequence and abundance. Author summary Tandem arrays of sequence repeats, or satellite DNA, makes up large and variable proportions of eukaryote genomes. Satellites may be an important component of genomes, but their evolution is not well understood because they are subject to a variety of different evolutionary forces due to their repetitive nature and proximity to centromeres, and they are difficult to sequence. Here we use a fruit fly Drosophila virilis – whose genome experienced a recent explosion in satellite DNA to make up 40+% of its genome – to understand the evolutionary processes that drive satellite composition. We found that the satellite emerged and expanded rapidly, and is variable among related species. The satellites have different patterns of evolution depending on their proximity to the centromere. We show evidence that the satellites may act selfishly and result in trade-offs on other satellites due to the push-back of selection.

Chimerical retroposition delineate a process by which RNA reverse transcribed integration into genome accompanied with recruiting flanking sequence, which is asserted to play essential roles and drive genome evolution. Although chimerical retrogenes hold high origination rate in plant genome, the evolutionary pattern of retrogenes and their parental genes are not well understood in rice genome. In this study, using maximum likelihood method, we evaluated the substitution ratio along lineages of 24 retrogenes and parental gene pairs to retrospect the evolutionary patterns. The results indicate that some specific lineages in 7 pairs underwent positive selection. Besides the rapid evolution in the initial stage of new chimerical retrogene evolution, an unexpected pattern was revealed: soon or some uncertain period after the origination of new chimerical retrogenes, their parental genes evolved rapidly under positive selection, rather than the rapid evolution of the new chimerical retrogenes themselves. This result lend support to the hypothesis that the new copy assistant the function evolution among parental gene and retrogene. Transcriptionally, we also found that one retrogene (RCG3) have a high expression at the period of calli infection which supported by chip data while its parental gene doesn’t have. Finally, by calibration to Ka/Ks analysis results in other species including Apis mellifera, we concluded that chimerical retrogenes are higher proportionally positive selected than the regular genes in the rice genome.

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However, their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction (0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons, and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.

New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river. Supplementary information The online version of this article (doi:10.1038/ng.3044) contains supplementary material, which is available to authorized users., The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. Supplementary information The online version of this article (doi:10.1038/ng.3044) contains supplementary material, which is available to authorized users.

Genes are perpetually added to and deleted from genomes during evolution. Thus, it is important to understand how new genes are formed and how they evolve to be critical components of the genetic systems that determine the biological diversity of life. Two decades of effort have shed light on the process of new gene origination and have contributed to an emerging comprehensive picture of how new genes are added to genomes, ranging from the mechanisms that generate new gene structures to the presence of new genes in different organisms to the rates and patterns of new gene origination and the roles of new genes in phenotypic evolution. We review each of these aspects of new gene evolution, summarizing the main evidence for the origination and importance of new genes in evolution. We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular, and phenotypic functions.

Genes that have originated in recent evolution are present in only a subset of organisms and are often assumed to be dispensable or redundant. This Review discusses our latest understanding of how new genes in diverse species have actually evolved to have important functions in diverse developmental and physiological processes in various organisms. During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.

In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation.

Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome2. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Our results suggest that evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.

Copy Number Variants (CNVs) underlie several genomic disorders and are a major source of genetic innovation. Consequently, any bias affecting their placement in the genome will impact our understanding of human disease and genome evolution. Here we report a mutational bias affecting CNVs that generates different probabilities of duplication and deletion across the genome in association with DNA replication time. We show that this mutational bias has important consequences for genome evolution by leading to different probabilities of gene duplication for different classes of genes and by linking the probability of gene duplication with the transcriptional activity of genes.

Insulin genes in mouse and rat compose a two-gene system in which Ins1 was retroposed from the partially processed mRNA of Ins2. When Ins1 originated and how it was retained in genomes still remain interesting problems. In this study, we used genomic approaches to detect insulin gene copy number variation in rodent species and investigated evolutionary forces acting on both Ins1 and Ins2. We characterized the phylogenetic distribution of the new insulin gene (Ins1) by Southern analyses and confirmed by sequencing insulin genes in the rodent genomes. The results demonstrate that Ins1 originated right before the mouse–rat split (∼20 MYA), and both Ins1 and Ins2 are under strong functional constraints in these murine species. Interestingly, by examining a range of nucleotide polymorphisms, we detected positive selection acting on both Ins2 and Ins1 gene regions in the Mus musculus domesticus populations. Furthermore, three amino acid sites were also identified as having evolved under positive selection in two insulin peptides: two are in the signal peptide and one is in the C-peptide. Our data suggest an adaptive divergence in the mouse insulin two-gene system, which may result from the response to environmental change caused by the rise of agricultural civilization, as proposed by the thrifty-genotype hypothesis.

Biologists are now able to investigate intricate biological systems by exploring the most fundamental source of biological information – the genome. In the last decades, there has been tremendous advance in sequencing and analyzing genomes from diverse organisms. Comparative analyses between genomes from different species provide a powerful strategy to understand how genomes function and evolve. Here, we argue that studying the origin of new genes can shed light on fundamental evolutionary questions. We illustrate this point by summarizing studies of new genes implicated in basic cellular processes, such as regulatory networks, cell division, and protein traffic.

Studies of gene evolution converge to understand the mechanisms, processes, evolutionary forces and phenotypic impacts underlying the origin and death of genes. Sex chromosomes have independently originated several times in nature, providing different genomic environments between males and female despite identical autosomal part of their genomes, which triggered and influenced the evolution of new genes with various functions and phenotypes. In this review, we aim to describe and discuss examples of heteromorphic sex chromosomes X, Y, Z, and W under gene evolution perspective.

To systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments.

This issue published a research article by Yang et al.[1] of Peking University “Significant divergence of sex-related non-coding RNA expression patterns among closely related species in Drosophila”. In a genomic analysis of D. melanogaster and its close relatives, D. simulans, D. yakuba and other related species, D. pseudoobscura and D. virillis, Yang et al. identified a dozen of gonad-(mostly testis-)expression non-coding RNA (ncRNA) genes. It is revealed that these ncRNA genes show diverged expression patterns in these species. The simple method used in the study can be efficiently applied to detection of ncRNA genes in a group of closely related species from a broad range of organisms. This comment will not reiterate experiments and interpretation in detail in this paper. Instead, we will put forward our emphasis on the discussion of the significance of related results in the understanding of biology and evolution of sex reproduction. We will discuss general significance of this work in development and education of the area of ncRNA genes.

Background The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. The mechanisms by which new genes are integrated into ancestral networks, and their evolutionary significance, are yet to be characterized. Herein, we present a study investigating the rates and patterns of new gene-driven evolution of GGI networks in the human and mouse genomes. Results We examine the network topological and functional evolution of new genes that originated at various stages in the human and mouse lineages by constructing and analyzing three different GGI datasets. We find a large number of new genes integrated into GGI networks throughout vertebrate evolution. These genes experienced a gradual integration process into GGI networks, starting on the network periphery and gradually becoming highly connected hubs, and acquiring pleiotropic and essential functions. We identify a few human lineage-specific hub genes that have evolved brain development-related functions. Finally, we explore the possible underlying mechanisms driving the GGI network evolution and the observed patterns of new gene integration process. Conclusions Our results unveil a remarkable network topological integration process of new genes: over 5000 new genes were integrated into the ancestral GGI networks of human and mouse; new genes gradually acquire increasing number of gene partners; some human-specific genes evolved into hub structure with critical phenotypic effects. Our data cast new conceptual insights into the evolution of genetic networks. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0772-4) contains supplementary material, which is available to authorized users.

A genomic pattern of new gene origination is often dependent on a genomic method that can efficiently identify a statistically adequate number of recently originated genes. The heterochromatic regions have often been viewed as genomic deserts with low coding potential and thus a low flux of new genes. However, increasing reports revealed unexpected roles of heterochromatic regions in the evolution of genes and genomes. We identified recently retroposed genes that originated in heterochromatic regions in Drosophila, by developing microarray-based comparative genomic hybridization (CGH) with multiple species. This new gene family, named Ifc-2h, originated in the common ancestor of the clade of D. simulans, D. mauritiana, and D. sechellia. The sequence features and phylogenetic distribution indicated that Ifc-2h resulted from the retroposition from its parental gene, Infertile crescent (Ifc), and integrated into heterochromatic region of common ancestor of the three sibling species 2 million years ago. Expression analysis revealed that Ifc-2h had developed a new expression pattern by recruiting a putative regulatory element from its target sequence. The distribution of indel variation in Ifc-2h of D. simulans and D. mauritiana revealed a significant sequence constraint, suggesting that the Ifc-2h gene may be functional. These analyses cast fresh insight into the evolution of heterochromatin and the origin of its coding regions.

Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

Exon shuffling is an essential molecular mechanism for the formation of new genes. Many cases of exon shuffling have been reported in vertebrate genes. These discoveries revealed the importance of exon shuffling in the origin of new genes. However, only a few cases of exon shuffling were reported from plants and invertebrates, which gave rise to the assertion that the intron-mediated recombination mechanism originated very recently. We focused on the origin of new genes by exon shuffling and retroposition. We will first summarize our experimental work, which revealed four new genes in Drosophila, plants, and humans. These genes are 106 to 108 million years old. The recency of these genes allows us to directly examine the origin and evolution of genes in detail. These observations show firstly the importance of exon shuffling and retroposition in the rapid creation of new gene structures. They also show that the resultant chimerical structures appearing as mosaic proteins or as retroposed coding structures with novel regulatory systems, often confer novel functions. Furthermore, these newly created genes appear to have been governed by positive Darwinian selection throughout their history, with rapid changes of amino acid sequence and gene structure in very short periods of evolution. We further analyzed the distribution of intron phases in three non-vertebrate species, Drosophila melanogaster, Caenorhabditis elegans, and Arabidosis thaliana, as inferred from their genome sequences. As in the case of vertebrate genes, we found that intron phases in these species are unevenly distributed with an excess of phase zero introns and a significant excess of symmetric exons. Both findings are consistent with the requirements for the molecular process of exon shuffling. Thus, these non-vertebrate genomes may have also been strongly impacted by exon shuffling in general.

The recent sequencing of several eukaryotic genomes has generated considerable interest in the study of gene duplication events. The classical model of duplicate gene evolution is that recurrent mutation ultimately results in one copy becoming a pseudogene, and only rarely will a beneficial new function evolve. Here, we study divergence between coding sequence duplications in Drosophila melanogaster as a function of the linkage relationship between paralogs. The mean K(a)/K(s) between all duplicates in the D. melanogaster genome is 0.2803, indicating that purifying selection is maintaining the structure of duplicate coding sequences. However, the mean K(a)/K(s) between duplicates that are both on the X chromosome is 0.4701, significantly higher than the genome average. Further, the distribution of K(a)/K(s) for these X-linked duplicates is significantly shifted toward higher values when compared with the distributions for paralogs in other linkage relationships. Two models of molecular evolution provide qualitative explanations of these observations-relaxation of selective pressure on the duplicate copies and, more likely, positive selection on recessive adaptations. We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes.

As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions – the origin and evolution of new genes – because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.

The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster . We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection.

Recent studies have revealed key roles of noncoding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these noncoding RNAs. Profiling the transcriptome of Drosophila melanogaster with whole-genome tiling arrays found that 15% of male-biased transcribed fragments are intergenic noncoding RNAs (incRNAs), suggesting a potentially important role for incRNAs in sex-related biological processes. Statistical analysis revealed a paucity of male-biased incRNAs and coding genes on the X chromosome, suggesting that similar evolutionary forces could be affecting the genomic organization of both coding and noncoding genes. Expression profiling across germline and somatic tissues further suggested that both male meiotic sex chromosome inactivation (MSCI) and sexual antagonism could contribute to the chromosomal distribution of male-biased incRNAs. Comparative sequence analysis showed that the evolutionary age of male-biased incRNAs is a significant predictor of their chromosomal locations. In addition to identifying abundant sex-biased incRNAs in the fly genome, our work unveils a global picture of the complex interplay between noncoding RNAs and sexual chromosome evolution.

The position of a gene in the genome may have important consequences for its function. Therefore, when a new duplicate gene arises, its location may be critical in determining its fate. Our recent work in humans, mouse, and Drosophila provided a test by studying the patterns of duplication in sex chromosome evolution. We revealed a bias in the generation and recruitment of new gene copies involving the X chromosome that has been shaped largely by selection for male germline functions. The gene movement patterns we observed reflect an ongoing process as some of the new genes are very young while others were present before the divergence of humans and mouse. This suggests a continuing redistribution of male-related genes to achieve a more efficient allocation of male functions. This notion should be further tested in organisms employing other sex determination systems or in organisms differing in germline sex chromosome inactivation. It is likely that the selective forces that were detected in these studies are also acting on other types of duplicate genes. As a result, future work elucidating sex chromosome differentiation by other mutational mechanisms will shed light on this important process.

Summary: gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset. It is especially useful for newly sequenced genomes that have not been well annotated. We applied gKaKs to estimate the genome-wide substitution rates in five pairs of closely related species. The average Ka and Ks computed by gKaKs were consistent with previous studies. We also compared the Ka, Ks and Ka/Ks of mouse and rat orthologous protein-coding genes estimated by gKaKs and based on the alignments generated by PAL2NAL. Results from two methods are compatible. Availability and implementation: gKaKs is implemented in Perl and is freely available on http://longlab.uchicago.edu/?q=gKaKs. The detailed user manual is available on the website. Contact: cfan@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Background Recent reports have highlighted instances of mRNAs that, in addition to coding for protein, regulate the abundance of related transcripts by altering microRNA availability. These two mRNA roles - one mediated by RNA and the other by protein - are inter-dependent and hence cannot easily be separated. Whether the RNA-mediated role of transcripts is important, per se, or whether it is a relatively innocuous consequence of competition by different transcripts for microRNA binding remains unknown. Results Here we took advantage of 48 loci that encoded proteins in the earliest eutherian ancestor, but whose protein-coding capability has since been lost specifically during rodent evolution. Sixty-five percent of such loci, which we term 'unitary pseudogenes', have retained their expression in mouse and their transcripts exhibit conserved tissue expression profiles. The maintenance of these unitary pseudogenes' spatial expression profiles is associated with conservation of their microRNA response elements and these appear to preserve the post-transcriptional roles of their protein-coding ancestor. We used mouse Pbcas4, an exemplar of these transcribed unitary pseudogenes, to experimentally test our genome-wide predictions. We demonstrate that the role of Pbcas4 as a competitive endogenous RNA has been conserved and has outlived its ancestral gene's loss of protein-coding potential. Conclusions These results show that post-transcriptional regulation by bifunctional mRNAs can persist over long evolutionary time periods even after their protein coding ability has been lost.

New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination.

New genes are a major source of genetic innovation in genomes. However, until recently, understanding how new genes originate and how they evolve was hampered by the lack of appropriate genetic datasets. The advent of the genomic era brought about a revolution in the amount of data available to study new genes. For the first time, decades-old theoretical principles could be tested empirically and novel and unexpected avenues of research opened up. This chapter explores how genomic data can and is being used to study both the origin and evolution of new genes and the surprising discoveries made thus far.

Comparative ChIP-seq data reveal adaptive evolution of insulator protein CTCF binding in multiple Drosophila species., Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression. However, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. Here we examine the genome-wide binding of CTCF in four species of Drosophila separated by between ∼2.5 and 25 million years. CTCF is a highly conserved protein known to be associated with insulator sequences in the genomes of human and Drosophila. Although the binding preference for CTCF is highly conserved, we find that CTCF binding itself is highly evolutionarily dynamic and has adaptively evolved. Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding sites. Newly evolved CTCF binding sites show a significantly stronger signature for positive selection than older sites. Comparative gene expression profiling revealed that expression divergence of genes adjacent to CTCF binding site is significantly associated with the gain and loss of CTCF binding. Further, the birth of new genes is associated with the birth of new CTCF binding sites. Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes., Author Summary A large proportion of the diversity of living organisms results from differential regulation of gene transcription. Transcriptional regulation is thought to differ between species because of evolutionary changes in the physical interactions between regulatory DNA elements and DNA-binding proteins; these can generate variation in the spatial and temporal patterns of gene expression. The mechanisms by which these protein–DNA interactions evolve is therefore an important question in evolutionary biology. Does adaptive evolution play a role, or is the process dominated by neutral genetic drift? Insulator proteins are a special group of DNA-binding proteins—instead of directly serving to activate or repress genes, they can function to coordinate the interactions between other regulatory elements (such as enhancers and promoters). Additionally, insulator proteins can limit the spreading of chromatin condensation and help to demarcate the boundaries of regulatory domains in the genome. In spite of their critical role in genome regulation, little is known about the evolution of interactions between insulator proteins and DNA. Here, we use ChIP-seq to examine the distribution of binding sites for CTCF, a highly conserved insulator protein, in four closely related Drosophila species. We find that genome-wide binding profiles of CTCF are highly dynamic across evolutionary time, with frequent births of new CTCF-DNA interactions, and we demonstrate that this evolutionary process is driven by natural selection. By comparing these with RNA-seq data, we find that gain or loss of CTCF binding impacts the expression levels of nearby genes and correlates with structural evolution of the genome. Together these results suggest a potential mechanism of regulatory re-wiring through adaptive evolution of CTCF binding.

Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases) but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. Here we take advantage of the Drosophila simulans–Drosophila melanogaster genetic system to further our understanding of both processes. Regarding mutational processes, the study of two closely related species allows investigation of the potential existence of shared duplication hotspots, and the similarities and differences between the two genomes can be used to dissect its underlying causes. Regarding selection, the difference in the effective population size between the two species can be leveraged to ask questions about the strength of selection acting on different classes of duplications. In this study, we conducted a survey of duplication polymorphisms in 14 different lines of D. simulans using tiling microarrays and combined it with an analogous survey for the D. melanogaster genome. By integrating the two datasets, we identified duplication hotspots conserved between the two species. However, unlike the duplication hotspots identified in mammalian genomes, Drosophila duplication hotspots are not associated with sequences of high sequence identity capable of mediating non-allelic homologous recombination. Instead, Drosophila duplication hotspots are associated with late-replicating regions of the genome, suggesting a link between DNA replication and duplication rates. We also found evidence supporting a higher effectiveness of selection on duplications in D. simulans than in D. melanogaster. This is also true for duplications segregating at high frequency, where we find evidence in D. simulans that a sizeable fraction of these mutations is being driven to fixation by positive selection., Author Summary DNA duplications are important contributors to the phenotypic differences observed between individuals. These mutations can disrupt the normal functioning of genes and so are often associated with disease. But because they can add genetic information they can also lead to evolutionary change. Understanding how selection and non-random mutation processes shape the distribution of duplications throughout the genome is important to elucidate both the medical and evolutionary impacts of these mutations. Here, we examined the roles of selection and mutation in shaping patterns of duplication polymorphisms across the genomes of the fruit fly Drosophila melanogaster and its sister species, D. simulans. We found that selection is pervasive in both genomes but is more efficient in D. simulans than in D. melanogaster. We also found that these two species have shared duplication hotspots, i.e. orthologous regions experiencing high rates of duplication in the two genomes. After excluding the hypothesis that Drosophila duplication hotspots are associated with regions of the genome rich in segmental duplications (as observed for mammalian genomes), we show that they are associated with late-replicating regions of the genome. Our work therefore proposes a link between DNA replication and rates of duplication across the genome.

Motivation: Retrocopies are important genes in the genomes of almost all higher eukaryotes. However, the annotation of such genes is a non-trivial task. Intronless genes have often been considered to be retroposed copies of intron-containing paralogs. Such categorization relies on the implicit premise that alignable regions of the duplicates should be long enough to cover exon–exon junctions of the intron-containing genes, and thus intron loss events can be inferred. Here, we examined the alternative possibility that intronless genes could be generated by partial DNA-based duplication of intron-containing genes in the fruitfly genome. Results: By building pairwise protein-, transcript- and genome-level DNA alignments between intronless genes and their corresponding intron-containing paralogs, we found that alignments do not cover exon–exon junctions in 40% of cases and thus no intron loss could be inferred. For these cases, the candidate parental proteins tend to be partially duplicated, and intergenic sequences or neighboring genes are included in the intronless paralog. Moreover, we observed that it is significantly less likely for these paralogs to show inter-chromosomal duplication and testis-dominant transcription, compared to the remaining 60% of cases with evidence of clear intron loss (retrogenes). These lines of analysis reveal that DNA-based duplication contributes significantly to the 40% of cases of single exon gene duplication. Finally, we performed an analogous survey in the human genome and the result is similar, wherein 34% of the cases do not cover exon–exon junctions. Thus, genome annotation for retrogene identification should discard candidates without clear evidence of intron loss. Contact: mlong@uchicago.edu; zhangy@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome.

The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

What constitutes genetic difference among organisms? How do new gene functions originate in nature? Since the early days of molecular biology, we have known that homologous genes between species differ in DNA and protein sequence. Noncoding regions have also been evolving with repetitive sequences, transposable elements, and other elements continuously reshaping genomes of organisms. As more genomes of humans and other organisms are examined, it also becomes clear that species differ not only in these two genomic parameters but also in the number and kinds of genes. Genes are subject to a life and death process: New genes have originated continuously throughout evolution. For example, Drosophila melanogaster contains 87 cuticle protein genes, while Caenorhabditis elegans contains no such genes in its genome (Rubin et al. 2000). If this is thought to be comparing toodivergent organisms, take a look at recently divergent sibling species. Drosophila teisseiri and Drosophila yakuba contain a gene called jingwei (Long and Langley 1993; Wang et al. 2000), which originated only 2.5 million years ago. D. melanogaster itself has a unique gene Sdic, which expresses particularly in the sperm tail and does not exist in even its closest relative species (Nurminsky et al. 1998). New genes often give rise to new biological functions driven by adaptive Darwinian selection (Long and Langley 1993; Chen et al. 1997; Begun 1997; Nurminsky et al. 1998). New genes may even have controlled the origination of new species, for example, Odysseus, a homeobox duplicate gene in Drosophila (Ting et al. 1998). Such new genes are associated with two conspicuous changes consistent with origin of new functions: High protein substitution rates and drastic changes in gene structure. Drosophila is not the only organism whose genome has been found to originate new protein-coding genes differentiating one species from another. Other organisms, including plants and mammals, also have newly originated genes. For example, the Mus musculus genome contains multiple copies of the new gene SP100-rs, which is absent in its sibling species Mus caroli (Weichenhan et al. 1998), though little detail of its evolution and function is known. In potato, a new cytochrome c1 originated a mitochondrial targeting function (Long et al. 1996). Retrosequences may have contributed to the origin of new vertebrate regulatory elements or new parts of vertebrate coding regions (Brosius 1999). In these cases, recombination of protein modules and gene duplication played essential roles in creating the initial gene structures, and natural selection participated in the subsequent evolution. Although insights from young chimerical genes in Drosophila have enormously changed our views of new gene evolution, good data from humans or mammals have been lacking. This is a significant hurdle for understanding new gene evolution in the genetic systems of the human and its primate relatives. In this issue, Thompson et al. (2000) present a clear example of how new genes with novel functions can originate in humans and other mammals, including the molecular process and derived biological function. A closer look at the origination of this new gene, Kua-UEV, offers insights into the general problem of human gene origination. UEV is a conserved gene, distributed across all major eukaryotic lineages ranging from animals to fungi, plants, and protozoa. The UEV proteins in these organisms share multiple functions, for example, cell protection, c-FOS transcription, and cell-cycle progression (Sancho et al. 1998; Thomson et al. 1998; Xiao et al. 1998). In Saccharomyces cerevisiae, the UEV protein controls elongation of polyubiquitin chains when associated with ubiquitin-conjugating enzymes (E2; Hoffman and Pickart 1999). The UEV genes in divergent organisms have maintained a very conserved structure in its common domain (C domain). However, there exists an additional domain (B domain) in one isoform of the human gene that does not exist in other organisms and, thus, creates a new, chimerical gene structure. How did this new structure originate, and where does the B domain come from? From the first glimpse, this human gene is reminiscent of the chimerical structure of two Drosophila young genes. The first example is jingwei, which is composed of a major domain and an additional N-terminal domain (Long and Langley 1993). Recent work implies that the mosaic structure of jingwei was created by insertion of the retrosequence of the alcohol dehydrogenase gene into a previously existing gene, recruiting a portion of the N-terminal domain (Long et al. 1999; Wang et al. 2000). The second example is Sdic, which was created by a deletion in two adjacent genes at the DNA level (Nurminsky et al. 1998). However, the human UEV gene seems to have taken a different evolutionary route to acquire its additional B domain (Fig. 1). In the genomic databases of D. melananogster and C. elegans, two small DNA fragments unrelated to the UEV gene in these species were found to be significantly similar to the B domain of the human UEV gene. Further analysis showed that these are seven exons encoding a 319–amino acid protein in C. elegans and five exons encoding a 326– amino acid protein in D. melanogaster. This newly discovered gene, named Kua (derived from the word “Cua” in Catalan, which means “tail” or “queue”) enE-MAIL mlong@midway.uchicago.edu; FAX (773)702-9740. Article and publication are at www.genome.org/cgi/ doi/10.1101/gr.165700 Insight/Outlook

Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of Oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago (MYA). For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.

How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant expression of intergenic ncRNAs. However, some reported that ncRNAs have been recently falsified, and, in general, the false positive rate for ncRNA detection is unknown. In this report, we used reverse transcription-PCR (RT-PCR), a more robust method, to detect ncRNAs from the intergenic regions that are expressed in four major developmental stages (6-8 h embryo, 20-22 h embryo, larvae and adult). We tested 1027 regions, approximately 10% of all intergenic regions, and detected transcription by RT-PCR. The results from 18 342 RT-PCR experiments revealed evidence for transcription in 72.7% of intergenic regions in the developmental process. The early developmental stage appears to be associated with more abundant ncRNAs than later developmental stages. In the early stage, we detected 43.6% of intergenic regions that encode transcripts in the triplicate RT-PCR experiments, yielding an estimate of 5006 intergenic regions in the entire genome likely encoding ncRNAs. We compared the RT-PCR-related approach with previous tiling array-based approach and observed that the latter method is insensitive to short ncRNAs, especially the molecules less than 120 bp. We measured false positive rates for the analyzed genomic approaches including the RT-PCR and tiling array method.

Gene copies that stem from the mRNAs of parental source genes have long been viewed as evolutionary dead-ends with little biological relevance. Here we review a range of recent studies that have unveiled a significant number of functional retroposed gene copies in both mammalian but also some non-mammalian genomes (in particular that of the fruitfly). These studies not only revealed previously unknown mechanisms for the emergence of new genes and their functions but also provided fascinating general insights into molecular and evolutionary processes that have shaped genomes. For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh new light on the evolutionary origin and biology of our sex chromosomes.

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Recent literature demonstrates that retrogenes tend to leave the X chromosome and integrate onto the autosomes and evolve male-biased expression patterns. Several selection-based evolutionary mechanisms have been proposed to explain this observation. Testing these selection-based models requires examining the evolutionary history and functional properties of new retrogenes, particularly those that show evidence of directional movement between the X and the autosomes (X-related retrogenes). This includes autosomal retrogenes with parental paralogs on the X chromosome (X-derived autosomal retrogenes) and those retrogenes integrated onto the X chromosomes (X-linked retrogenes). In order to understand why retrogenes tend to move nonrandomly in genomes, we examined the expression patterns and evolutionary mechanisms concerning gene pairs having young retrogenes--originating less than 20 MYA (after mouse-rat split). We demonstrate that these X-derived autosomal retrogenes evolved a more restricted male-biased expression pattern: they are expressed exclusively or predominantly in the testis, in particular, during the late stages of spermatogenesis. In contrast, the parental counterparts have relatively broad expression patterns in various tissues and spermatogenetic stages. We further observed that positive selection is targeting these X-derived autosomal retrogenes with novel male-biased expression patterns. This suggests that such retrogenes evolved new male germ-line functions that may be complementary to the functions of the parental paralogs, which themselves contribute little during spermatogenesis. Such evolutionary changes may be beneficial to the populations. Furthermore, most identified X-related retrogenes have recruited novel adjacent sequences as their untranslated regions (UTRs), suggesting that these UTRs, acquired de novo, may play an important role in establishing new regulatory mechanisms to carry out the new male germ-line functions.

Comparative genomics is rapidly bringing to light the manifold differences that exist within and between species on the molecular level. Of fundamental interest are the absolute and relative amounts of the genome dedicated to protein coding regions. Results thus far have shown surprising variation on both the polymorphism and divergence levels. As a result, there has been an increase in efforts aimed to characterize the underlying genetic mechanisms and evolutionary forces that continue to alter genomic architecture. In this review we discuss the formation of chimeric genes generated at the DNA level. While the formation of chimeric genes has been shown to be an important way in which coding regions of the genome evolve, many of the detailed studies have been limited to chimeric genes formed through retroposition events (through an RNA intermediate step). Here we provide a short review of the reported mechanisms that have been identified for chimeric gene formations, excluding retroposition-related cases, and discuss several of the evolutionary analyses carried out on them. We emphasize the utility chimeric genes provide for the study of novel function. We also emphasize the importance of studying chimeric genes that are evolutionarily young.

Recent genomic analyses in Drosophila and mammals of inter-chromosomal retroposition have revealed that during evolution the retroposed genes that show male-biased expression tend to leave the X chromosome and opt for autosomal positions. Such a phenomenon may be a process of general, genomic and evolutionary relevance. It contributed to the unexpected overrepresentation of male-biased genes on the autosomes recently observed in microarray expression experiments. In this paper, we report our genomic analysis of within-chromosomal retroposition in Drosophila melanogaster, and compare it with the previously identified pattern of the between-chromosomal retroposition. We find that a surfeit of autosomal retroposed genes originated from parental genes located on the same chromosome, in contrast to the X chromosome in which only few genes retroposed in cis. Such an autosomal proximity effect implicates a role of the mutation process for retroposition in determining chromosomal locations of autosome-derived retroposed genes. Furthermore, this phenomenon supports the hypothesis that natural selection favors the retroposition of genes out of the X chromosome. Analyses of a large expression database for D. melanogaster genes revealed that the vast majority of the X-derived autosomal retroposed genes had evolved testis expression functions, consistent with other previous genomic analyses.

Udgivelsesdato: Aug Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species