Recently mobilized transposons in the human and chimpanzee genomes

Transposable genetic elements are abundant in the genomes of most organisms, including humans. These endogenous mutagens can alter genes, promote genomic rearrangements, and may help to drive the speciation of organisms. In this study, we identified almost 11,000 transposon copies that are differentially present in the human and chimpanzee genomes. Most of these transposon copies were mobilized after the existence of a common ancestor of humans and chimpanzees, approximately 6 million years ago. Alu, L1, and SVA insertions accounted for >95% of the insertions in both species. Our data indicate that humans have supported higher levels of transposition than have chimpanzees during the past several million years and have amplified different transposon subfamilies. In both species, approximately 34% of the insertions were located within known genes. These insertions represent a form of species-specific genetic variation that may have contributed to the differential evolution of humans and chimpanzees. In addition to providing an initial overview of recently mobilized elements, our collections will be useful for assessing the impact of these insertions on their hosts and for studying the transposition mechanisms of these elements.     

Concerted evolution of members of the multisequence family chAB4 located on various nonhomologous chromosomes

During the last years it became obvious that a lot of families of long-range repetitive DNA elements are located within the genomes of mammals. The principles underlying the evolution of such families, therefore, may have a greater impact than anticipated on the evolution of the mammalian genome as a whole. One of these families, called chAB4, is represented with about 50 copies within the human and the chimpanzee genomes and with only a few copies in the genomes of gorilla, orang-utan, and gibbon. Members of chAB4 are located on 10 different human chromosomes. FISH of chAB4-specific probes to chromosome preparations of the great apes showed that chAB4 is located, with only one exception, at orthologous places in the human and the chimpanzee genome. About half the copies in the human genome belong to two species-specific subfamilies that evolved after the divergence of the human and the chimpanzee lineages. The analysis of chAB4-specific PCR-products derived from DNA of rodent/human cell hybrids showed that members of the two human-specific subfamilies can be found on 9 of the 10 chAB4-carrying chromosomes. Taken together, these results demonstrate that the members of DNA sequence families can evolve as a unit despite their location at multiple sites on different chromosomes. The concerted evolution of the family members is a result of frequent exchanges of DNA sequences between copies located on different chromosomes. Interchromosomal exchanges apparently take place without greater alterations in chromosome structure. Received: 20 March 1997 / Accepted: 13 September 1997     

Bifurcation and Enhancement of Autonomous-Nonautonomous Retrotransposon Partnership through LTR Swapping in Soybean

Long terminal repeat (LTR) retrotransposons, the most abundant genomic components in flowering plants, are classifiable into autonomous and nonautonomous elements based on their structural completeness and transposition capacity. It has been proposed that selection is the major force for maintaining sequence (e.g., LTR) conservation between nonautonomous elements and their autonomous counterparts. Here, we report the structural, evolutionary, and expression characterization of a giant retrovirus-like soybean (Glycine max) LTR retrotransposon family, SNARE. This family contains two autonomous subfamilies, SARE^A and SARE^B, that appear to have evolved independently since the soybean genome tetraploidization event ∼13 million years ago, and a nonautonomous subfamily, SNRE, that originated from SARE^A. Unexpectedly, a subset of the SNRE elements, which amplified from a single founding SNRE element within the last ∼3 million years, have been dramatically homogenized with either SARE^A or SARE^B primarily in the LTR regions and bifurcated into distinct subgroups corresponding to the two autonomous subfamilies. We uncovered evidence of region-specific swapping of nonautonomous elements with autonomous elements that primarily generated various nonautonomous recombinants with LTR sequences from autonomous elements of different evolutionary lineages, thus revealing a molecular mechanism for the enhancement of preexisting partnership and the establishment of new partnership between autonomous and nonautonomous elements.     

Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages

Using 40 known human-specific LTR sequences, we have derived a consensus sequence for an evolutionary young HERV-K (HML-2) LTR family, which was named the HS family. In the human genome the HS family is represented by approximately 150-160 LTR sequences, 90% of them being human-specific (hs). The family can be subdivided into two subfamilies differing in five linked nucleotide substitutions: HS-a and HS-b of 5.8 and 10.3 Myr evolutionary ages, respectively. The HS-b subfamily members were transpositionally active both before the divergence of the human and chimpanzee ancestor lineages and after it in both lineages. The HS-a subfamily comprises only hs LTRs. These and other data strongly suggest that at least three "master genes" of HERV-K (HML-2) LTRs were active in the human ancestor lineage after the human-chimpanzee divergence. We also found hs HERV-K (HML-2) LTRs integrations in introns of 12 human genes and identified 13 new hs HERV-K (HML-2) LTRs.     

SVA elements: a hominid-specific retroposon family

SVA is a composite repetitive element named after its main components, SINE, VNTR and Alu. We have identified 2762 SVA elements from the human genome draft sequence. Genomic distribution analysis indicates that the SVA elements are enriched in G+C-rich regions but have no preferences for inter- or intragenic regions. A phylogenetic analysis of the elements resulted in the recovery of six subfamilies that were named SVA_A to SVA_F. The composition, age and genomic distribution of the subfamilies have been examined. Subfamily age estimates based upon nucleotide divergence indicate that the expansion of four SVA subfamilies (SVA_A, SVA_B, SVA_C and SVA_D) began before the divergence of human, chimpanzee and gorilla, while subfamilies SVA_E and SVA_F are restricted to the human lineage. A survey of human genomic diversity associated with SVA_E and SVA_F subfamily members showed insertion polymorphism frequencies of 37.5% and 27.6%, respectively. In addition, we examined the amplification dynamics of SVA elements throughout the primate order and traced their origin back to the beginnings of hominid primate evolution, approximately 18 to 25 million years ago. This makes SVA elements the youngest family of retroposons in the primate order.     

Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution.     

Replicon fusions promoted by the inverted repeats of Tn5. The right repeat is an insertion sequence

Members of three repetitive sequence families were isolated from recombinant λ-genome libraries, and were used to investigate sequence relationships within these families. Studies presented elsewhere show that members of all three repeat sequence families are transcribed tissue-specifically. The thermal stability of intrafamilial heteroduplexes was measured, and the extent of colinearity between related sequences was determined by restriction mapping, heteroduplex visualization, gel blot hybridization, and direct sequencing. One large and very divergent family, named 2108, was shown to consist of an assemblage of many small repeat sequence subfamilies. Each subfamily includes <40 members which are not contiguous in the genome but are very closely related colinear sequence elements several thousand nucleotides in length. The different 2108 subfamilies share only small sequence subelements, which in each subfamily occur in a different linear order and are surrounded by different sequences. A second divergent family consisting of short repetitive sequences, the 2109 family, includes many small internally homologous subfamilies as well. A third family, 2034, displays little internal sequence divergence and no apparent subfamily structure. The repeat sequence subfamilies may be biologically significant units of repetition. Thus specific 2108 subfamilies were shown to be evolutionary conserved to a remarkable degree. Highly homologous 2108 sequences were found shared among sea urchin species which diverged almost 200 million years ago, although only about 10% of the single copy DNA sequences of these species are now homologous enough to crossreact.     

A young Alu subfamily amplified independently in human and African great apes lineages.

A variety of Alu subfamilies amplified in primate genomes at different evolutionary time periods. Alu Sb2 belongs to a group of young subfamilies with a characteristic two-nucleotide deletion at positions 65/66. It consists of repeats having a 7-nucleotide duplication of a sequence segment involving positions 246 through 252. The presence of Sb2 inserts was examined in five genomic loci in 120 human DNA samples as well as in DNAs of higher primates. The lack of the insertional polymorphism seen at four human loci and the absence of orthologous inserts in apes indicated that the examined repeats retroposed early in the human lineage, but following the divergence of great apes. On the other hand, similar analysis of the fifth locus (butyrylcholinesterase gene) suggested contemporary retropositional activity of this subfamily. By a semi-quantitative PCR, using a primer pair specific for Sb2 repeats, we estimated their copy number at about 1500 per human haploid genome; the corresponding numbers in chimpanzee and gorilla were two orders of magnitude lower, while in orangutan and gibbon the presence of Sb2 Alu was hardly detectable. Sequence analysis of PCR-amplified Sb2 repeats from human and African great apes is consistent with the model in which the founding of Sb2 subfamily variants occurred independently in chimpanzee, gorilla and human lineages.     

Molecular evolution of P transposable elements in the genus Drosophila. I. The saltans and willistoni species groups

A phylogenetic survey using the polymerase chain reaction (PCR) has identified four major P element subfamilies in the saltans and willistoni species groups of Drosophila. One subfamily, containing about half of the sequences studied, consists of elements that are very similar to the canonical (and active) P element from D. melanogaster. Within this subfamily, nucleotide sequence differentiation among different copies from the same species and among elements from different species is relatively low. This observation suggests that the canonical elements are relatively recent additions to the genome or, less likely, are evolving slowly relative to the other subfamilies. Elements belonging to the three noncanonical lineages are distinct from the canonical elements and from one another. Furthermore, there is considerably more sequence variation, on the average, within the noncanonical subfamilies compared to the canonical elements. Horizontal transfer and the coexistence of multiple, independently evolving element subfamilies in the same genome may explain the distribution of P elements in the saltans and willistoni species groups. Such explanations are not mutually exclusive, and each may be involved to varying degrees in the maintenance of P elements in natural populations of Drosophila.      

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Different Rates of LINE-1 (L1) Retrotransposon Amplification and Evolution in New World Monkeys

LINE-1 (L1) elements constitute the major family of retrotransposons in mammalian genomes. Here we report the first investigation of L1 evolution in New World monkeys (NWM). Two regions of the second open-reading frame were analyzed by two methods in three NWM species, the squirrel monkey (Saimiri sciureus), the tamarin (Saguinus oedipus), and the spider monkey (Ateles paniscus). Since these three species diverged, L1 has amplified in the Saimiri and Saguinus lineages but L1 activity seems to have been strongly reduced in the Ateles lineage. In addition, the active L1 lineage has evolved rapidly in Saimiri and Saguinus, generating species-specific subfamilies. In contrast, we found no evidence for a species-specific subfamily in Ateles, a result consistent with the low L1 activity in this species for the last ~25 My.     

Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates.

Over the past 60 million years, or so, approximately one million copies of Alu DNA repeats have accumulated in the genome of primates, in what appears to be an ongoing process. We determined the phylogenetic distribution of specific Alu (and other) DNA repeats in the genome of several primates: human, chimpanzee, gorilla, orangutan, baboon, rhesus, and macaque. At the population level studied, the majority of the repeats was found to be fixed in the primate species. Our data suggest that new Alu elements arise in unique, irreversible events, in a mechanism that seems to preclude precise excision and loss. The same insertions did not arise independently in two species. Once inserted and genetically fixed, the DNA elements are retained in all descendant lineages. The irreversible expansion of Alu s introduces a vector of time into the evolutionary process, and provides realistic (rather than statistical) answers to questions on phylogenies. In contrast to point mutations, the present distribution of individual Alu s is congruent with just one phylogeny. We submit that only irreversible and taxonomically relevant events are at the molecular basis of evolution. Most point mutations do not belong to this category.     

The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.

G protein-coupled receptor kinases (GRKs) desensitize G protein-coupled receptors by phosphorylating activated receptors. The six known GRKs have been classified into three subfamilies based on sequence and functional similarities. Examination of the mouse GRK4 subfamily (GRKs 4, 5, and 6) suggests that mouse GRK4 is not alternatively spliced in a manner analogous to human or rat GRK4, whereas GRK6 undergoes extensive alternative splicing to generate three variants with distinct carboxyl termini. Characterization of the mouse GRK 5 and 6 genes reveals that all members of the GRK4 subfamily share an identical gene structure, in which 15 introns interrupt the coding sequence at equivalent positions in all three genes. Surprisingly, none of the three GRK subgroups (GRK1, GRK2/3, and GRK4/5/6) shares even a single intron in common, indicating that these three subfamilies are distinct gene lineages that have been maintained since their divergence over 1 billion years ago. Comparison of the amino acid sequences of GRKs from various mammalian species indicates that GRK2, GRK5, and GRK6 exhibit a remarkably high degree of sequence conservation, whereas GRK1 and particularly GRK4 have accumulated amino acid changes at extremely rapid rates over the past 100 million years. The divergence of individual GRKs at vastly different rates reveals that strikingly different evolutionary pressures apply to the function of the individual GRKs.     

Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons

Background  

Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. In this study, subfamilies falling on the AluYi and AluYh lineages, and the AluYg6 subfamily, are assessed for the presence of secondary source genes, and the influence of gene conversion on the AluYh and AluYi lineages is also described.     

Evolution of the master Alu gene(s)

Summary A comparison of Alu sequences that comprise more recently amplified Alu subfamilies was made. There are 18 individual diagnostic mutations associated with the different subfamilies. This analysis confirmed that the formation of each subfamily can be explained by the sequential accumulation of mutations relative to the previous subfamily. Polymerase chain reaction amplification of orthologous loci in several primate species allowed us to determine the time of insertion of Alu sequences in individual loci. These data suggest that the vast majority of Alu elements amplified at any given time comprised a single Alu subfamily. We find that, although the individual divergence relative to a consensus sequence correlate reasonably well with sequence age, the diagnostic mutations are a more accurate measure of the age of any individual Alu family member. Our data are consistent with a model in which all Alu family members have been made from a single master gene or from a series of sequential master genes. This master gene(s) accumulated diagnostic base changes, resulting in the amplification of different subfamilies from the master gene at different times in primate evolution. The changes in the master gene(s) probably occurred individually, but their appearance is clearly punctuated. Ten of them have occurred within an 15-million-year time span, 40–25 million years ago, and 8 changes have occurred within the last 5 million years. Surprisingly, no changes appeared in the 20 milion years separating these periods.     

Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity

Centromeric retrotransposons (CR) are located almost exclusively at the centromeres of plant chromosomes. Analysis of the emerging Zea mays inbred B73 genome sequence revealed two novel subfamilies of CR elements of maize (CRM), bringing the total number of known CRM subfamilies to four. Orthologous subfamilies of each of these CRM subfamilies were discovered in the rice lineage, and the orthologous relationships were demonstrated with extensive phylogenetic analyses. The much higher number of CRs in maize versus Oryza sativa is due primarily to the recent expansion of the CRM1 subfamily in maize. At least one incomplete copy of a CRM1 homolog was found in O. sativa ssp. indica and O. officinalis, but no member of this subfamily could be detected in the finished O. sativa ssp. japonica genome, implying loss of this prolific subfamily in that subspecies. CRM2 and CRM3, as well as the corresponding rice subfamilies, have been recently active but are present in low numbers. CRM3 is a full-length element related to the non-autonomous CentA, which is the first described CRM. The oldest subfamily (CRM4), as well as its rice counterpart, appears to contain only inactive members that are not located in currently active centromeres. The abundance of active CR elements is correlated with chromosome size in the three plant genomes for which high quality genomic sequence is available, and the emerging picture of CR elements is one in which different subfamilies are active at different evolutionary times. We propose a model by which CR elements might influence chromosome and genome size. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents

LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.