共查询到20条相似文献,搜索用时 15 毫秒
1.
It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available. 相似文献
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Analysis of ungulate bones recovered from a number of Upper and Middle Palaeolithic sites in southern Italy revealed differences in the presence of anatomical elements. There is a lack of clear evidence of carnivore activities, and differences can be attributed to human activity. Indeed, these differences were probably due to different patterns of skeletal exploitation between Homo neanderthalensis and H. sapiens. Small limb bones (carpals, tarsals, sesamoids, long bone epiphyses and especially phalanges) are rarely found in Middle Palaeolithic deposits, but are abundant in the Upper Palaeolithic. The observation of unidentified bone fragments at these sites indicates that during the middle Palaeolithic, marrow extraction regarded essentially the treatment of long bones. First and second phalanges were not frequently used for this practice, but they were often fragmented by H. sapiens. Lack of these bones among the remains of meals of Neanderthal suggests that these bones were probably destroyed by their utilisation as fuel. 相似文献
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Adriana Granzotto Fabrício R Lopes Emmanuelle Lerat Cristina Vieira Claudia MA Carareto 《BMC evolutionary biology》2009,9(1):174-11
Background
Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster), whereas putatively active sequences are present in others (D. simulans). Combining experimental and population analyses with the sequence analysis of the 12 Drosophila genomes, we have investigated the evolution of Helena, and propose a possible scenario for the evolution of this element. 相似文献6.
Elena Barghini Lucia Natali Tommaso Giordani Rosa Maria Cossu Simone Scalabrin Federica Cattonaro Hana ?imková Jan Vrána Jaroslav Dole?el Michele Morgante Andrea Cavallini 《DNA research》2015,22(1):91-100
Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms. 相似文献
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Five Drosophila genomes reveal nonneutral evolution and the signature of host specialization in the chemoreceptor superfamily 总被引:2,自引:1,他引:2
The insect chemoreceptor superfamily comprises the olfactory receptor (Or) and gustatory receptor (Gr) multigene families. These families give insects the ability to smell and taste chemicals in the environment and are thus rich resources for linking molecular evolutionary and ecological processes. Although dramatic differences in family size among distant species and high divergence among paralogs have led to the belief that the two families evolve rapidly, a lack of evolutionary data over short time scales has frustrated efforts to identify the major forces shaping this evolution. Here, we investigate patterns of gene loss/gain, divergence, and polymorphism in the entire repertoire of approximately 130 chemoreceptor genes from five closely related species of Drosophila that share a common ancestor within the past 12 million years. We demonstrate that the overall evolution of the Or and Gr families is nonneutral. We also show that selection regimes differ both between the two families as wholes and within each family among groups of genes with varying functions, patterns of expression, and phylogenetic histories. Finally, we find that the independent evolution of host specialization in Drosophila sechellia and D. erecta is associated with a fivefold acceleration of gene loss and increased rates of amino acid evolution at receptors that remain intact. Gene loss appears to primarily affect Grs that respond to bitter compounds while elevated Ka/Ks is most pronounced in the subset of Ors that are expressed in larvae. Our results provide strong evidence that the observed phenomena result from the invasion of a novel ecological niche and present a unique synthesis of molecular evolutionary analyses with ecological data. 相似文献
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The gtwin retrotransposon was recently discovered in the Drosophila
melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal
transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length
Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work. 相似文献
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C B Ruff 《American journal of physical anthropology》1984,65(4):347-358
Allometric equations relating length and cross-sectional geometric properties of the femur and tibia are generated using skeletal remains from three recent human population samples. Approximate isometry, or geometric similarity, is found both within and between samples. Cross-sectional areas scale to approximately length2, while second moments of area scale to approximately length4. It is shown that this is consistent with the maintenance of equivalent mechanical stress in long bones of different length under dynamic loadings in vivo. Other evidence indicates that bending and torsional loadings are more critical than axial loadings in the determination of lower limb bone cross-sectional dimensions. 相似文献
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The bilbo element is a non-LTR retrotransposon isolated from Drosophila subobscura. We conducted a distribution survey by Southern blot for 52 species of the family Drosophilidae, mainly from the obscura and melanogaster groups. Most of the analyzed species bear sequences homologous to bilbo from D. subobscura. In the obscura group, species from the same species subgroup also share similar Southern blot patterns. To investigate the phylogenetic relationship among these elements, we analyzed eight copies of a short sequence of the element from several species of the obscura group. The obtained phylogram agrees with the phylogeny of the species, which suggests vertical transmission of the element. 相似文献
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Hughes AL 《Molecular phylogenetics and evolution》2004,30(2):287-294
Genomes of the four plant viruses of the genus Nanovirus consist of multiple circular single-stranded DNA components, each of which encodes a single protein. Protein phylogenies supported the hypothesis that faba bean necrotic yellows virus (FBNYV) and milk vetch disease virus (MDV) are sister taxa; that subterranean clover stunt virus (SCSV) branched next; and that banana bunchy top virus (BBTV) is an outgroup to the three other species. The phylogeny of replication (Rep) proteins indicate that this small viral multi-gene family has evolved by a process of duplication and subsequent loss of Rep-encoding genome components, analogous to the "birth-and-death" process of evolution which has been described in eukaryotic multi-gene families. By contrast, repeated recombinational events between components were found to have homogenized the non-coding portions of several components encoding unrelated components. For example, as result of recent recombination a portion of the non-coding region is virtually identical among SCSV components 1, 3, 4, 5, and 7. Thus, there is a process of concerted evolution of non-coding regions of Nanovirus genome components, which raises the possibility that certain non-coding regions are subject to functional constraint. 相似文献
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Untranslated regions (UTRs) in eukaryotes play a significant role in the regulation of translation and mRNA half-life, as well as interacting with specific RNA-binding proteins. However, UTRs receive less attention than more crucial elements such as genes, and the basic structural and evolutionary characteristics of UTRs of different species, and the relationship between these UTRs and the genome size and species gene number is not well understood. To address these questions, we performed a comparative analysis of 5' and 3' untranslated regions of different species by analyzing the basic characteristics of 244,976 UTRs from three eukaryote kingdoms (Plantae, Fungi, and Protista). The results showed that the UTR lengths and SSR frequencies in UTRs increased significantly with increasing species gene number while the length and G+C content in 5' UTRs and different types of repetitive sequences in 3' UTRs increased with the increase of genome size. We also found that the sequence length of 5' UTRs was significantly positively correlated with the presence of transposons and SSRs while the sequence length of 3' UTRs was significantly positively correlated with the presence of tandem repeat sequences. These results suggested that evolution of species complexity from lower organisms to higher organisms is accompanied by an increase in the regulatory complexity of UTRs, mediated by increasing UTR length, increasing G+C content of 5' UTRs, and insertion and expansion of repetitive sequences. 相似文献
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Transposable elements (TEs) are indwelling components of genomes, and their dynamics have been a driving force in genome evolution. Although we now have more information concerning their amounts and characteristics in various organisms, we still have little data from overall comparisons of their sequences in very closely-related species. While the Drosophila melanogaster genome has been extensively studied, we have only limited knowledge regarding the precise TE sequences in the genomes of the related species Drosophila simulans, Drosophila sechellia and Drosophila yakuba. In this study we analyzed the number and structure of TE copies in the sequenced genomes of these four species. Our findings show that, unexpectedly, the number of TE insertions in D. simulans is greater than that in D. melanogaster, but that most of the copies in D. simulans are degraded and in small fragments, as in D. sechellia and D. yakuba. This suggests that all three species were invaded by numerous TEs a long time ago, but have since regulated their activity, as the present TE copies are degraded, with very few full-length elements. In contrast, in D. melanogaster, a recent activation of TEs has resulted in a large number of almost-identical TE copies. We have detected variants of some TEs in D. simulans and D. sechellia, that are almost identical to the reference TE sequences in D. melanogaster, suggesting that D. melanogaster has recently been invaded by active TE variants from the other species. Our results indicate that the three species D. simulans, D. sechellia, and D. yakuba seem to be at a different stage of their TE life cycle when compared to D. melanogaster. Moreover, we show that D. melanogaster has been invaded by active TE variants for several TE families likely to come from D. simulans or the ancestor of D. simulans and D. sechellia. The numerous horizontal transfer events implied to explain these results could indicate introgression events between these species. 相似文献
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Jacek Tomczyk 《Human Evolution》2006,21(3-4):203-213
The origins of Homo sapiens is a central issue of modern paleoanthropology. The available fossil material serves as a basis for postulating different
hypotheses and models, but as is widely appreciated, anthropologists have yet to reach a consensus about human origins. It
seems possible that the main reasons behind such an irreducible divergence of opinions are different methodological approaches
rather than the analyses of fossil material. Some scientists would say that it is the fragmentary nature of fossil material
which accounts for the debates about the origins of H. sapiens. Had the debate been only a matter of the empirical considerations many disagreements concerning H. sapiens would have probably disappeared long ago. But since the controversies are imbued in methodological reality the closure of
the debate is not to be expected soon. There are three research methods: morphological, archaeological and genetic. Each approach
has a specific definition of H. sapiens at its disposal, which largely accounts for the different scenarios for the origin of our species. Any debate concerning
this problem must therefore begin with a discussion about the research methods. The controversy about our origins thus appears
to be of secondary importance. The present paper aims at presenting the methodological controversy in relation to the origins
of H. sapiens. The discussion about the genealogy of H. sapiens certainly is in urgent need of a new, more integrated way of approaching the past. 相似文献
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Two Drosophila pseudoobscura genomic clones have sequence similarity to the Drosophila melanogaster amylase region that maps to the 53CD region on the D. melanogaster cytogenetic map. The two clones with similarity to amylase map to sections 73A and 78C of the D. pseudoobscura third chromosome cytogenetic map. The complete sequences of both the 73A and 78C regions were compared to the D. melanogaster genome to determine if the coding region for amylase is present in both regions and to determine the evolutionary mechanism responsible for the observed distribution of the amylase gene or genes. The D. pseudoobscura 73A and 78C linkage groups are conserved with the D. melanogaster 41E and 53CD regions, respectively. The amylase gene, however, has not maintained its conserved linkage between the two species. These data indicate that amylase has moved via a transposition event in the D. melanogaster or D. pseudoobscura lineage. The predicted genes within the 73A and 78C regions show patterns of molecular evolution in synonymous and nonsynonymous sites that are consistent with previous studies of these two species. 相似文献
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The nucleotide sequences of the 5'-flanking regions of the duplicated Amy
genes in eight sibling species belonging to the melanogaster species
subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp
immediately upstream of the translation initiation site of the two
paralogous genes (the proximal and distal genes) has sequence similarities.
However, we could not detect any significant sequence similarity in the
region more upstream than -450. This result indicates that the coding
regions of the ancestral Amy gene were duplicated together with 450 bp of
the 5'-flanking region as one unit. Multiple alignment of these 450-bp
sequences in the proximal and distal genes of all eight species revealed a
mosaic pattern of highly conserved and divergent regions. The conserved
regions included almost all the putative regulatory elements identified in
previous analyses of the sequences. A phylogenetic analysis of the aligned
sequences shows that these 450-bp sequences are clustered into the proximal
and the distal groups. As a whole, the divergence between groups in this
region is very large in contrast to that in the coding regions. Based on
the divergence between groups, the 450-bp region is divided into two
subregions. We found that the ratios of the divergence between groups to
that within groups differ in the two subregions. From these observations,
we discuss a possibility of positive selection acting on the subregion
immediately upstream of the Amy coding region to cause divergence of
regulatory elements of the paralogous genes.
相似文献
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We have sequenced the long terminal direct repeats (and adjacent DNA) of two members of the 412 family of transposable elements of Drosophila melanogaster cloned on fragments of DNA from strain Oregon R. The repeats of the first element are identical and 481 base-pairs long; the repeats of the second are also identical but are 571 base-pairs long. The first 482 base-pairs of the 571 base-pair sequence correspond to the 481 base-pair repeat differing by five base substitutions and one addition/deletion. The 571 base-pair repeats are rare. Each of these 412 elements is flanked by a four base-pair direct repeat, suggesting that insertion of a 412 element is associated with duplication of four base-pairs. Analysis of the “empty site” from strain Canton S corresponding to one of these elements supports this conclusion. The sequence of 481 base-pair repeats and of 412 DNA immediately adjacent to them show striking similarities to corresponding regions of vertebrate proviruses and we discuss the implications this may have for the mechanism of transposition. 相似文献