Genomic analysis of Drosophila melanogaster telomeres: full-length copies of HeT-A and TART elements at telomeres

The repetitive nature of heterochromatin hampers its analysis in general genome-sequencing projects. Specific studies are needed to extend the sequence into telomeric and centromeric heterochromatin. Drosophila telomeres lack the telomerase-generated repeats that are characteristic of other eukaryotic chromosomes. Instead, they consist of tandem arrays of HeT-A and TART elements. Herein, we present the genomic organization of the telomeres in the isogenic strain (y; cn bw sp) that was used for the Drosophila melanogaster sequencing project. The data indicate that the canonical features of telomere organization are widely conserved in evolution. In addition, we have identified full-length elements, likely competent elements, for HeT-A and TART.     

Evolutionary conservation,diversity and specificity of LTR‐retrotransposons in flowering plants: insights from genome‐wide analysis and multi‐specific comparison

The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross‐species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 long terminal repeat‐retrotransposon (LTR‐RT) families comprising 32 370 elements in soybean (Glycine max (L.) Merr.). Approximately 87% of these elements were located in recombination‐suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that of chromosome arms (1.62). Further analysis revealed a significant positive correlation between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed seven Copia and five Gypsy evolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, a Copia lineage has been lost in soybean. Analysis of the physical association of LTR‐RTs with centromere satellite repeats identified two putative centromere retrotransposon (CR) families of soybean, which were grouped into the CR (e.g. CRR and CRM) lineage found in grasses, indicating that the ‘functional specification’ of CR pre‐dates the bifurcation of eudicots and monocots. However, a number of families of the CR lineage are not concentrated in centromeres, suggesting that their CR roles may now be defunct. Our data also suggest that the envelope‐like genes in the putative Copia retrovirus‐like family are probably derived from the Gypsy retrovirus‐like lineage, and thus we propose the hypothesis of a single ancient origin of envelope‐like genes in flowering plants.     

The Genomic HyperBrowser: inferential genomics at the sequence level

The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no.     

Genomic analyses and the origin of the eukaryotes

The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the 'tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or 'ring' rather than a 'tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes.     

Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.     

Genomic distribution of the retrovirus-like element ZAM in Drosophila

The mobile element ZAM, recently identified in Drosophila melanogaster, is similar in structure and coding potential to vertebrate retroviruses. In this paper, we analyze the insertional and structural polymorphism of this element and show that members of this family appear to have a long evolutionary history in the genome of Drosophila. It is present in all the species of the D. melanogaster subgroup and in more distantly related species like D. takahashii, D. ananassae, or D. virilis but in a lower copy number or with a lower homology. Two categories of strains have been previously identified in D. melanogaster: strains with a high copy number of ZAM and strains with a low copy number. Here, we show that ZAM is at least in a low copy number in each tested strain of the species analyzed. The study of ZAM's genomic distribution by FISH mapping analysis to salivary gland polytene chromosomes or on mitotic chromosomes indicates that most of the insertion sites of ZAM elements are associated with the constitutive heterochromatin regardless of the ZAM copy number. In addition, our results suggest that multiple ZAM elements are present at the insertion sites visualized by in situ experiments. This revised version was published online in August 2006 with corrections to the Cover Date.     

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis.     

The origin of nematode sperm: Progenesis at the cellular level

Analysis of the development and structure of aberrant sperm of nematodes and other metazoans with internal insemination showed that these spermatozoa have several unusual, but shared features: (1) the absence of a flagellum and an axoneme, an unusual arrangement of centrioles; (2) an amoeboid shape and amoeboid motility due to cytoskeleton components; (3) the poor condensation of nuclear chromatin, which may be diffuse, thread-like, and discrete; (4) the absence of a nuclear envelope; (5) multiple unmodified mitochondria; (6) the absence of an acrosome; (7) unique membranous components derived from the Golgi complex; and (8) the large size of spermatozoa due to prominent cytoplasm filled with a great number of components. These shared features of aberrant spermatozoa may be explained by the conservation of a number of features that are characteristic of the primitive undifferentiated cell (the predecessor of all specialized gametes). The primitive cell features of numerous versions of aberrant sperm reflect the arrest of cytoplasm specialization of male gametes at an early stage of development. This pattern of gamete evolution is quite consistent with the conception of progenesis (retention of juvenile characters by precocious, sexually mature morphologically juvenile stage). Thus, the origin of the aberrant sperm of nematodes and many other metazoans may be interpreted as progenesis at the cellular level.     

Genomic structure of human polyoma virus JC: nucleotide sequence of the region containing replication origin and small-T-antigen gene

The nucleotide sequence of the region of human polyoma virus JC DNA between 0.5 and 0.7 map units from a unique EcoRI cleavage site was determined and compared with those of the corresponding regions of another human polyoma virus, BK, and simian virus 40 DNAs. Within this region consisting of 945 base pairs, we located the origin of DNA replication near 0.7 map units, the entire coding region for small T antigen, and the splice junctions for large-T-antigen mRNA. The deduced amino acid sequences for small T antigen and the part of large T antigen markedly resembled those of polyoma virus BK and simian virus 40. The results strongly suggest that polyoma virus JC has the same organization of early genome as polyoma virus BK and simian virus 40 on the physical map, with the EcoRI site as a reference point.     

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale,Merino and Creole sheep

The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip^®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F_ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F_ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F_ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.     

Genomic signatures of the plateless phenotype in the threespine stickleback

Understanding the genetic basis of traits involved in adaptive divergence and speciation is one of the most fundamental objectives in evolutionary biology. Toward that end, we look for signatures of extreme plate loss in the genome of freshwater threespine sticklebacks (Gasterosteus aculeatus). Plateless stickleback have been found in only a few lakes and streams across the world; they represent the far extreme of a phenotypic continuum (plate number) that has been studied for years, although plateless individuals have not yet been the subject of much investigation. We use a dense single nucleotide polymorphism dataset made using RADseq to study fish from three freshwater populations containing plateless and low plated individuals, as well as fish from full plated marine populations. Analyses were performed using FastStructure, sliding windows F_ST, Bayescan and latent factor mixed models to search for genomic differences between the low plated and plateless phenotypes both within and among the three lakes. At least 18 genomic regions which may contribute to within‐morph plate number variation were detected in our low plated stickleback populations. We see no evidence of a selective sweep between low and plateless fish; rather reduction of plate number within the low plated morph seems to be polygenic.     

Genomic signatures of local adaptation in the Drosophila immune response

As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.     

Plasma lipidomics reveals potential prognostic signatures within a cohort of cystic fibrosis patients

Cystic fibrosis (CF) is associated with abnormal lipid metabolism. We have recently shown variations in plasma levels of several phosphatidylcholine (PC) and lysophopshatidylcholine (LPC) species related to disease severity in CF patients. Here our goal was to search for blood plasma lipid signatures characteristic of CF patients bearing the same mutation (F508del) and different phenotypes, and to study their correlation with forced expiratory volume in 1 s (FEV1) and Pseudomonas aeruginosa chronic infection, evaluated at the time of testing (t = 0) and three years later (t = 3). Samples from 44 F508del homozygotes were subjected to a lipidomic approach based on LC-ESI-MS. Twelve free fatty acids were positively correlated with FEV1 at t = 0 (n = 29). Four of them (C20:3n-9, C20:5n-3, C22:5n-3, and C22:6n-3) were also positively correlated with FEV1 three years later, along with PC(32:2) and PC(36:4) (n = 31). Oleoylethanolamide (OEA) was negatively correlated with FEV1 progression (n = 17). Chronically infected patients at t = 0 showed lower PC(32:2), PC(38:5), and C18:3n-3 and higher cholesterol, cholesterol esters, and triacylglycerols (TAG). Chronically infected patients at t = 3 showed significantly lower levels of LPC(18:0). These results suggest a potential prognostic value for some lipid signatures in, to our knowledge, the first longitudinal study aimed at identifying lipid biomarkers for CF.     

Characterisation of DNA methylation status using spectroscopy (mid‐IR versus Raman) with multivariate analysis

Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier‐transform infrared (ATR‐FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5‐methylcytosine, cytosine and guanine bases. Applied to Low‐E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline‐corrected and vector normalised over the 1750 cm^–1–760 cm^–1 (for ATR‐FTIR spectroscopy) or the 1750 cm^–1–600 cm^–1 (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)