G-Anchor:A novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences

Background Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses. Results Here we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species? reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours, and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. Conclusions G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences, and that are not highly repetitive, polypoid or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available via https://github.com/vasilislenis/G-AnchorpublishersversionPeer reviewe

SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole-genome sequence

<p>Abstract</p> <p>Background</p> <p>The recent availability of genomic sequences and BAC libraries for a large number of mammals provides an excellent opportunity for identifying comparatively-anchored markers that are useful for creating high-resolution radiation-hybrid (RH) and BAC-based comparative maps. To use these maps for multispecies genome comparison and evolutionary inference, robust bioinformatic tools are required for the identification of chromosomal regions shared between genomes and to localize the positions of evolutionary breakpoints that are the signatures of chromosomal rearrangements. Here we report an automated tool for the identification of homologous synteny blocks (HSBs) between genomes that tolerates errors common in RH comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution.</p> <p>Findings</p> <p>We developed an algorithm and software tool (SyntenyTracker) that can be used for automated definition of HSBs using pair-wise RH or gene-based comparative maps as input. To verify correct implementation of the underlying algorithm, SyntenyTracker was used to identify HSBs in the cattle and human genomes. Results demonstrated 96% agreement with HSBs defined manually using the same set of rules. A comparison of SyntenyTracker with the AutoGRAPH synteny tool was performed using identical datasets containing 14,380 genes with 1:1 orthology in human and mouse. Discrepancies between the results using the two tools and advantages of SyntenyTracker are reported.</p> <p>Conclusion</p> <p>SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies. The utility of SyntenyTracker will become more important for comparative genomics as the number of mapped and sequenced genomes increases.</p

Fluctuation-Driven First-Order Transition in Pauli-limited d-wave Superconductors

We study the phase transition between the normal and non-uniform (Fulde-Ferrell-Larkin-Ovchinnikov) superconducting state in quasi two-dimensional d-wave superconductors at finite temperature. We obtain an appropriate Ginzburg-Landau theory for this transition, in which the fluctuation spectrum of the order parameter has a set of minima at non-zero momenta. The momentum shell renormalization group procedure combined with dimensional expansion is then applied to analyze the phase structure of the theory. We find that all fixed points have more than one relevant directions, indicating the transition is of the fluctuation-driven first order type for this universality class.Comment: 5 page

Reversal of Nonlocal Vortex Motion in the Regime of Strong Nonequilibrium

We investigate nonlocal vortex motion in weakly pinning a-NbGe nanostructures, which is driven by a transport current I and remotely detected as a nonlocal voltage Vnl. At high I, the measured Vnl exhibits dramatic sign reversals that at low and high temperatures T occur for opposite polarities of I. The sign of Vnl becomes independent of that of the drive current at large abs(I). These unusual effects can be nearly quantitatively explained by a novel enhancement of magnetization, arising from a nonequilibrium distribution of quasiparticles at high T, and a Nernst-like effect resulting from local electron heating at low T

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically

Nonlocal vs local vortex dynamics in the transversal flux transformer effect

In this follow-up to our recent Letter [F. Otto et al., Phys. Rev. Lett. 104, 027005 (2010)], we present a more detailed account of the superconducting transversal flux transformer effect (TFTE) in amorphous (a-)NbGe nanostructures in the regime of strong nonequilibrium in local vortex motion. Emphasis is put on the relation between the TFTE and local vortex dynamics, as the former turns out to be a reliable tool for determining the microscopic mechanisms behind the latter. By this method, a progression from electron heating at low temperatures T to the Larkin-Ovchinnikov effect close to the transition temperature Tc is traced over a range 0.26 < T/Tc < 0.95. This is represented by a number of relevant parameters such as the vortex transport entropy related to the Nernst-like effect at low T, and a nonequilibrium magnetization enhancement close to Tc. At intermediate T, the Larkin-Ovchinnikov effect is at high currents modified by electron heating, which is clearly observed only in the TFTE

Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

BACKGROUND: Bidirectional promoters are shared regulatory regions that influence the expression of two oppositely oriented genes. This type of regulatory architecture is found more frequently than expected by chance in the human genome, yet many specifics underlying the regulatory design are unknown. Given that the function of most orthologous genes is similar across species, we hypothesized that the architecture and regulation of bidirectional promoters might also be similar across species, representing a core regulatory structure and enabling annotation of these regions in additional mammalian genomes. RESULTS: By mapping the intergenic distances of genes in human, chimpanzee, bovine, murine, and rat, we show an enrichment for pairs of genes equal to or less than 1,000 bp between their adjacent 5' ends ("head-to-head") compared to pairs of genes that fall in the same orientation ("head-to-tail") or whose 3' ends are side-by-side ("tail-to-tail"). A representative set of 1,369 human bidirectional promoters was mapped to orthologous sequences in other mammals. We confirmed predictions for 5' UTRs in nine of ten manual picks in bovine based on comparison to the orthologous human promoter set and in six of seven predictions in human based on comparison to the bovine dataset. The two predictions that did not have orthology as bidirectional promoters in the other species resulted from unique events that initiated transcription in the opposite direction in only those species. We found evidence supporting the independent emergence of bidirectional promoters from the family of five RecQ helicase genes, which gained their bidirectional promoters and partner genes independently rather than through a duplication process. Furthermore, by expanding our comparisons from pairwise to multispecies analyses we developed a map representing a core set of bidirectional promoters in mammals. CONCLUSION: We show that the orthologous positions of bidirectional promoters provide a reliable guide to directly annotate over one thousand regulatory regions in sequences of mammalian genomes, while also serving as a useful tool to predict 5' UTR positions and identify genes that are novel to a single species

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

The file attached is the Published/publisher’s pdf version of the article.Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.NHM Repositor