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PubMed2000

Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans.

To examine the potential regulatory involvement of retroelements in the human genome, we screened the transcribed sequences of GenBank and expressed sequence tag data bases with long terminal repeat (LTR) elements derived from different human endogenous retroviruses. These screenings detected human transcripts containing LTRs belonging to the human endogenous retrovirus-E family fused to the apolipoprotein CI (apoC-I) and the endothelin B receptor (EBR) genes. However, both genes are known to have non-LTR (native) promoters. Initial reverse transcription-polymerase chain reaction experiments confirmed and authenticated the presence of transcripts from both the native and LTR promoters. Using a 5'-rapid amplification of cDNA ends protocol, we showed that the alternative transcripts of apoC-I and EBR are initiated and promoted by the LTRs. The LTR-apoC-I fusion and native apoC-I transcripts are present in many of the tissues tested. As expected, we found apoC-I preferentially expressed in liver, where about 15% of the transcripts are derived from the LTR promoter. Transient transfections suggest that the expression is not dependent on the LTR itself, but the presence of the LTR increases activity of the apoC-I promoter from both humans and baboons. The native EBR-driven transcripts were also detected in many tissues, whereas the LTR-driven transcripts appear limited to placenta. In contrast to the LTR of apoC-I, the EBR LTR promotes a significant proportion of the total EBR transcripts, and transient transfection results indicate that the LTR acts as a strong promoter and enhancer in a placental cell line. This investigation reports two examples where LTR sequences contribute to increased transcription of human genes and illustrates the impact of mobile elements on gene and genome evolution.

Alternative Splicing↗
PubMed2005

Identification of a short interspersed repeat in the Reticulitermes lucifugus (Isoptera Rhinotermitidae) genome.

A SINE element (called Talua) has been isolated from Reticulitermes lucifugus genome, by means of sequence comparison between clones obtained through genomic restriction and aspecific PCR amplification. It posses all the structural features commonly found in short interspersed elements: (i) a RNA polymerase III internal promoter, (ii) flanking short direct repeats and (iii) a poly (A) tail. BLAST search reveals significant homology with other previously described SINEs and tRNAs. The repeats are G+C-rich, but they are located in A+T-rich regions. This biased genomic distribution results from the analysis of adjacent regions. A Talua element was also found in a microsatellite-containing clone from Cryptotermes secundus. The presence of the SINE also in the Kalotermitidae family, suggests the usefulness of Talua as a taxonomic marker at the family level. The importance of this element on termite genome evolution is discussed.

Animals↗
PubMed2004

Testing the phylogenetic position of a parasitic plant (Cuscuta, Convolvulaceae, asteridae): Bayesian inference and the parametric bootstrap on data drawn from three genomes.

Previous findings on structural rearrangements in the chloroplast genome of Cuscuta (dodder), the only parasitic genus in the morning-glory family, Convolvulaceae, were attributed to its parasitic life style, but without proper comparison to related nonparasitic members of the family. Before molecular evolutionary questions regarding genome evolution can be answered, the phylogenetic problems within the family need to be resolved. However, the phylogenetic position of parasitic angiosperms and their precise relationship to nonparasitic relatives are difficult to infer. Problems are encountered with both morphological and molecular evidence. Molecular data have been used in numerous studies to elucidate relationships of parasitic taxa, despite accelerated rates of sequence evolution. To address the question of the position of the genus Cuscuta within Convolvulaceae, we generated a new molecular data set consisting of mitochondrial (atpA) and nuclear (RPB2) genes, and analyzed these data together with an existing chloroplast data matrix (rbcL, atpB, trnL-F, and psbE-J), to which an additional chloroplast gene (rpl2) was added. This data set was analyzed with an array of phylogenetic methods, including Bayesian analysis, maximum likelihood, and maximum parsimony. Further exploration of data was done by using methods of phylogeny hypothesis testing. At least two nonparasitic lineages are shown to diverge within the Convolvulaceae before Cuscuta. However, the exact sister group of Cuscuta could not be ascertained, even though many alternatives were rejected with confidence. Caution is therefore warranted when interpreting the causes of molecular evolution in Cuscuta. Detailed comparisons with nonparasitic Convolvulaceae are necessary before firm conclusions can be reached regarding the effects of the parasitic mode of life on patterns of molecular evolution in Cuscuta.

Base Sequence↗
PubMed2002

Nitric oxide and Mycobacterium leprae pathogenicity.

Leprosy is an old, still dreaded infectious disease caused by the obligate intracellular bacterium Mycobacterium leprae. During the infectious process, M. leprae is faced with the host macrophagic environment, where the oxidative stress and NO release, combined with low pH, low pO2, and high pCO2, contribute to limit the growth of the bacilli. Comparative genomics has unraveled massive gene decay in M. leprae, linking the strictly parasitic lifestyle with the reductive genome evolution. Compared with Mycobacterium tuberculosis and Mycobacterium bovis, the leprosy bacillus has lost most of the genes involved in the detoxification of reactive oxygen and nitrogen species. The very low reactivity of the unique truncated hemoglobin retained by M. leprae could account for the susceptibility of this exceptionally slow-growing microbe to NO.

Mycobacterium leprae↗
PubMed1989

DNA hybridization in animal taxonomy: a critique from first principles.

DNA hybridization is a "distance method" for phylogenetic reconstruction and, as such, shares a set of assumptions, advantages, and problems with other techniques that do not directly employ character data. The technique purports to measure the average percent mismatch of homologous nucleotide sequences between the single-copy genomes of species. This measurement, as any other, is subject to considerations of accuracy and precision. While replicate measurements and technical modifications can improve precision, the accuracy of such measurements is limited by the equivalence of genomes under comparison. Such routine events in genome evolution as gene duplication and deletion may complicate the interpretation of DNA hybridization distances. Beyond measurement limitations, the most serious potential distortions of distances are due to biased sequence sampling and homoplasy. These problems, however, do not necessarily preclude phylogenetic reconstruction, and their effects may be mitigated by numerical corrections. Homoplasy, in particular, is a difficulty faced by all methods of phylogenetic inference. If such distortions can be eliminated, mitigated by correction, or shown to be trivial, pairwise tree-construction strategies should provide reliable estimates of phylogeny.

Animals↗
PubMed2004

Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species.

BACKGROUND AND AIMS: The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. METHODS: A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. KEY RESULTS: Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. CONCLUSIONS: Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group.

Crosses, Genetic↗
PubMed2006

Biological applications of the theory of birth-and-death processes.

In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.

Animals↗
PubMed2002

PlantSat: a specialized database for plant satellite repeats.

MOTIVATION: Tandemly organized repetitive sequences (satellite DNA) are widespread in complex eukaryotic genomes. In plants, satellite repeats often represent a substantial part of nuclear DNA but only a little is known about the molecular mechanisms of their amplification and their possible role(s) in genome evolution and function. Unfortunately, addressing these questions via characterization of general sequence properties of known satellite repeats has been hindered by a difficulty in obtaining a complete and unbiased set of sequence data for this analysis. This is mainly due to the presence of multiple entries of homologous sequences and of single entries that contain more than one repeated unit (monomer) in the public databases. RESULTS: We have established a computer database specialized for plant satellite repeats (PlantSat) that integrates sequence data available from various resources with supplementary information including repeat consensus sequences, abundances, and chromosomal localizations. The sequences are stored as individual repeat monomers grouped into families, which simplifies their computer analysis and makes it more accurate. Using this feature, we have performed a basic sequence analysis of the whole set of plant satellite repeats with respect to their monomer length and nucleotide composition. The analysis revealed several preferred length ranges of the monomers (approximately 165 bp and its multiples) and an over-representation of the AA/TT dinucleotide in the repeats. We have also detected an enrichment of satellite DNA sequences for the motif CAAAA that is supposed to be involved in breakage-reunion of repeated sequences.

Computational Biology↗
PubMed2006

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

MOTIVATION: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains. RESULTS: Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method. AVAILABILITY: DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

Algorithms↗
PubMed2025

Post-translational modifications of the nucleoid protein H-NS: sites, mechanisms, and regulatory cues.

Histone-like nucleoid structuring protein H-NS plays a pivotal role in orchestrating bacterial chromatin and regulating horizontal gene transfer (HGT) elements. In response to environmental signals, H-NS undergoes dynamic post-translational modifications (PTMs) that resemble the epigenetic codes of eukaryotic histones. This review explores how environmental cues regulate PTMs at specific sites within distinct domains of H-NS, thereby modulating its oligomerization and DNA-binding capabilities to reprogram bacterial responses. Notably, HGT elements commonly encode counter-silencing factors, including PTM-modifying enzymes, that counteract H-NS repression. We propose that combinatorial PTM patterns on H-NS form the bacterial histone-like epigenetic code, regulating the expression of HGT elements. Collectively, these interactions establish a sophisticated network of silencing and counter-silencing mechanisms that drive bacterial genome evolution.

Protein Processing, Post-Translational↗
PubMed1997

The maize transposable element Ac induces recombination between the donor site and an homologous ectopic sequence.

The prominent repair mechanism of DNA double-strand breaks formed upon excision of the maize Ac transposable element is via nonhomologous end joining. In this work we have studied the role of homologous recombination as an additional repair pathway. To this end, we developed an assay whereby beta-Glucuronidase (GUS) activity is restored upon recombination between two homologous ectopic (nonallelic) sequences in transgenic tobacco plants. One of the recombination partners carried a deletion at the 5' end of GUS and an Ac or a Ds element inserted at the deletion site. The other partner carried an intact 5' end of the GUS open reading frame and had a deletion at the 3' end of the gene. Based on GUS reactivation data, we found that the excision of Ac induced recombination between ectopic sequences by at least two orders of magnitude. Recombination events, visualized by blue staining, were detected in seedlings, in pollen and in protoplasts. DNA fragments corresponding to recombination events were recovered exclusively in crosses with Ac-carrying plants, providing physical evidence for Ac-induced ectopic recombination. The occurrence of ectopic recombination following double-strand breaks is a potentially important factor in plant genome evolution.

Base Sequence↗
PubMed2000

A selective sweep associated with a recent gene transposition in Drosophila miranda.

In Drosophila miranda, a chromosome fusion between the Y chromosome and the autosome corresponding to Muller's element C has created a new sex chromosome system. The chromosome attached to the ancestral Y chromosome is transmitted paternally and hence is not exposed to crossing over. This chromosome, conventionally called the neo-Y, and the homologous neo-X chromosome display many properties of evolving sex chromosomes. We report here the transposition of the exuperantia1 (exu1) locus from a neo-sex chromosome to the ancestral X chromosome of D. miranda. Exu1 is known to have several critical developmental functions, including a male-specific role in spermatogenesis. The ancestral location of exu1 is conserved in the sibling species of D. miranda, as well as in a more distantly related species. The transposition of exu1 can be interpreted as an adaptive fixation, driven by a selective advantage conferred by its effect on dosage compensation. This explanation is supported by the pattern of within-species sequence variation at exu1 and the nearby exu2 locus. The implications of this phenomenon for genome evolution are discussed.

Alleles↗
PubMed1997

The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs.

The CMT1A-REPs are two large directly repeating DNA sequences located on chromosome 17p11.2-p12 flanking the region duplicated in patients with Charcot-Marie-Tooth disease type 1A (CMT1A) and deleted in patients with hereditary neuropathy with liability to pressure palsies (HNPP). We have sequenced two cosmids, c74F4 and c15H12, which contain the entire proximal and distal CMT1A-REPs and determined that these repeats are approximately 99% identical across a 24,011 bp region. In addition, both contain an exon of the human heme A:farnesyltransferase gene (COX10). Hybridization studies revealed that COX10 spans the distal CMT1A-REP, while the proximal CMT1A-REP contains an isolated COX10 'pseudo-exon'. There is also a COX10 hybridization signal on chromosome 10 which appears to represent a processed pseudogene. We propose that the distal CMT1A-REP represents the progenitor copy of COX10 exon VI which was duplicated with surrounding intronic sequences during mammalian genome evolution and that the HNPP deletion results in a COX10 null allele.

Alkyl and Aryl Transferases↗
PubMed2026

ntSynt-viz: Visualizing synteny patterns across multiple genomes.

With the explosion of chromosome-scale genome assemblies being generated in recent years, there is vast potential for comparative genomics analyses through detecting multi-genome synteny. While existing tools can detect synteny blocks between multiple genomes, their text-based outputs make it challenging to intuitively explore large-scale synteny patterns. Interpretable, information-rich and easy-to-use synteny visualization tools are imperative to enable important biological insights from the synteny block data output by the aforementioned utilities. Here, we present ntSynt-viz, a command-line tool for automated sorting, normalization and plotting of multi-genome synteny blocks. We show how ntSynt-viz provides clearer and more easily interpretable chromosome painting ribbon plots compared to the state-of-the-art tools NGenomeSyn and plotsr when evaluating synteny between 14 human genomes, and compared to NGenomeSyn when comparing 9 hoverfly genomes. As plotsr is limited to comparing genomes with equal chromosome numbers, it was not applicable to the hoverfly dataset. Furthermore, we demonstrate how ntSynt-viz can also be applied to visualize syntenic patterns encoded in pangenome graphs, using a Minigraph-Cactus graph built from 16 Drosophila genomes. We expect that ntSynt-viz will provide crucial insights into large-scale synteny patterns between divergent genomes, thereby advancing research into key evolutionary questions.

Synteny↗
PubMedDate not supplied

Physical mapping of rRNA genes in Medicago sativa and M. glomerata by fluorescent in situ hybridization.

Fluorescent in situ hybridization (FISH) was applied to diploid and tetraploid subspecies of alfalfa (Medicago sativa L.) to investigate the distribution of rRNA genes and to utilize the sites of 18S-5.8S-25S rDNA and 5S rDNA sequences as markers for studying the genome evolution within the species. Medicago glomerata Balb., the species considered to be the ancestor of alfalfa, was included in this study in order to obtain more information on the phylogenetics of alfalfa. Simultaneous in situ hybridization was performed with the probes pTa71 and pXVI labeled with digoxigenin and biotin, respectively. In the diploid taxa, M. glomerata, M. sativa ssp. coerulea Schmalh and ssp. falcata Arcangeli, the 18S-5.8S-25S rDNA sequences were mapped to two sites corresponding to the secondary constrictions of the nucleolar chromosome pair, while 5S rDNA appeared to be distributed in two pairs of sites. Chromosomes carrying 5S loci could be distinguished on the basis of their morphological characteristics. The number of rDNA sites detected in the tetraploid M. sativa ssp. falcata and ssp. sativa (L.) L. & L. were twice the number found in the respective diploid ssp. falcata and ssp. coerulea. The results of this study show that the distribution of ribosomal genes was maintained during the evolutionary steps from the primitive diploid to the cultivated alfalfa. Modifications of the number of rRNA loci were not observed. The importance of in situ hybridization for improving karyotype analysis in M. sativa L. is discussed.

Genes, rRNA↗
PubMed2026

Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica).

We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a BUSCO completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.

Canidae↗
PubMed2004

The control of copy number of IS6110 in Mycobacterium tuberculosis.

Insertion sequence (IS) elements are bacterial genes that are able to transpose to different locations in the genome. These elements are often used in molecular epidemiology as genetic markers that track the spread of pathogens. Transposable elements have frequently been described as "selfish DNA" because they facilitate their own transposition, causing damage when they insert into coding regions, while contributing little if anything to the bacterial host. According to this hypothesis, the expansion of copy number of insertion sequences is opposed by negative selection against high copy numbers. From an alternative point of view, we might expect IS elements to intrinsically regulate transposition within cells, thereby limiting damage to their bacterial host. Here, we report evidence that the copy number of IS6110 in Mycobacterium tuberculosis is controlled by selection against the element. We first construct 12 different models of marker change resulting from a combination of possible transposition functions and selective regimes. We then compute the Akaike Information Criterion for each model to identify the models that best explain data consisting of serial isolates of M. tuberculosis genotyped with IS6110. We find that the best performing models all include selection against the accumulation of copies. Specifically, our analysis points to the interaction of separate copies of the element causing lethal effects. We discuss the implications of these findings for genome evolution and molecular epidemiology.

DNA Transposable Elements↗
PubMed2006

Bats with hATs: evidence for recent DNA transposon activity in genus Myotis.

Transposable elements make up a significant fraction of many eukaryotic genomes. Although both classes of transposable elements, the DNA transposons and the retrotransposons, show substantial expansion in plants and invertebrates, the DNA transposons are thought to have become inactive in mammalian genomes long ago. Here, we report the first evidence for recent activity of DNA transposons in a mammalian lineage, the bat genus Myotis. Six recently active families of nonautonomous hobo/Activator/TAM transposons were identified in the Myotis lucifugus genome using computational tools. Low sequence divergence among the individual sequences and between individual sequences and their respective consensus sequences suggest their recent expansion in the M. lucifugus genome. Furthermore, amplification and sequencing of polymorphic insertion loci in a related taxon, M. austroriparius, confirms their recent activity. Myotis is one of the largest mammalian genera with 103 species. The discovery of DNA transposon activity in this genus may therefore influence our understanding of genome evolution and diversification in bats and in mammals in general. Furthermore, the identification of a likely autonomous element may lead to new approaches for mammalian genetic manipulation.

Animals↗