EST-based identification of genes expressed in the liver of adult seabass (Dicentrarchus labrax, L.)

The scarcity of the genomic resources for some fish species, in spite of their commercial interest, could retard the positive effects that modern biotechnology can offer to aquaculture industry. Then an effort should be made to reduce, as far as it concerns genomic resources, the gap that separates farming species from "model organisms". In this paper, we present an EST project in which we performed single pass sequencing on 1229 randomly selected clones from a sea bass cDNA library. The sequences are deposited in the NCBI database with the following accession numbers: from , from , from and from . EST cataloguing and profiling of seabass will set the basis for functional genomic research in this species, but will also serve for comparative and environmental genomics, for the identification of polymorphic markers useful, for example, to survey the disease resistance of fish, for the discovery of new molecular markers of exposure and for the production of micro- and macro-arrays.     

Synthesis of saporin gene probes from partial protein sequence data Use of inosine-oligonucleotides, genomic DNA and the polymerase chain reaction

Summary A strategy employing the polymerase chain reaction to synthesize gene-specific probes suitable for genomic Southern analyses and for screening genomic libraries is described. The method utilizes partial amino acid sequence data from the protein of interest, genomic DNA and inosine-containing oligonucleotide primers. An example of its application for the isolation of plant gene sequences encoding saporin, a ribosome inactivating protein, is described.     

GenomeDiagram: a python package for the visualization of large-scale genomic data

SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.     

Partitioning of population genetic variance under multiplicative-epistatic gene action

Determining the way in which different QTLs interact (epistasis) in their effects on the phenotype is crucial to many areas in population genetics and evolutionary biology. For example, in the founder event, a separated population readapts to a new environment through the release of cryptic gene-gene interactions. In hybrid zones, hybrid speciation must be subjected to natural selection for epistasis resulting from genomic recombinations between different species. However, there is a severe shortage of relevant methodologies to estimate epistatic genetic effects and variances. A statistical model has recently been proposed to estimate the number of QTLs, their genetic effects and allelic frequencies in segregating populations. This model is based on multiplicative gene action and derived from a two-level intra- and interspecific mating design. In this paper, we formulate a statistical procedure for partitioning the genetic variance into additive, dominant and various kinds of epistatic components in an intra- or mixed intra- and interspecific hybrid population. The procedure can be used to study the genetic architecture of fragmented populations and hybrid zones, thus allowing for a better recognition of the role of epistasis in evolution and hybrid speciation. A real example for two Populus species, P. tremuloides and P. tremula, is provided to illustrate the procedure. In this example, we found that considerable new genetic variation is formed through genomic recombination between two aspen species. Received: 1 May 1999 / Accepted: 27 July 1999     

Efficient multiple genome alignment

MOTIVATION: To allow a direct comparison of the genomic DNA sequences of sufficiently similar organisms, there is an urgent need for software tools that can align more than two genomic sequences. RESULTS: We developed new algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221 approximately bp.) is produced in 30 minutes.     

Exon discovery by genomic sequence alignment

MOTIVATION: During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating 'junk DNA' so local sequence similarity often indicates biological functionality. This fact can be used to identify functional elements in large eukaryotic DNA sequences by cross-species sequence comparison. In recent years, several gene-prediction methods have been proposed that work by comparing anonymous genomic sequences, for example from human and mouse. The main advantage of these methods is that they are based on simple and generally applicable measures of (local) sequence similarity; unlike standard gene-finding approaches they do not depend on species-specific training data or on the presence of cognate genes in data bases. As all comparative sequence-analysis methods, the new comparative gene-finding approaches critically rely on the quality of the underlying sequence alignments. RESULTS: Herein, we describe a new implementation of the sequence-alignment program DIALIGN that has been developed for alignment of large genomic sequences. We compare our method to the alignment programs PipMaker, WABA and BLAST and we show that local similarities identified by these programs are highly correlated to protein-coding regions. In our test runs, PipMaker was the most sensitive method while DIALIGN was most specific. AVAILABILITY: The program is downloadable from the DIALIGN home page at http://bibiserv.techfak.uni-bielefeld.de/dialign/.     

GWAsimulator: a rapid whole-genome simulation program

SUMMARY: GWAsimulator implements a rapid moving-window algorithm to simulate genotype data for case-control or population samples from genomic SNP chips. For case-control data, the program generates cases and controls according to a user-specified multi-locus disease model, and can simulate specific regions if desired. The program uses phased genotype data as input and has the flexibility of simulating genotypes for different populations and different genomic SNP chips. When the HapMap phased data are used, the simulated data have similar local LD patterns as the HapMap data. As genome-wide association (GWA) studies become increasingly popular and new GWA data analysis methods are being developed, we anticipate that GWAsimulator will be an important tool for evaluating performance of new GWA analysis methods. AVAILABILITY: The C++ source code, executables for Linux, Windows and MacOS, manual, example data sets and analysis program are available at http://biostat.mc.vanderbilt.edu/GWAsimulator     

Rolling circle amplification of genomic templates for inverse PCR (RCA–GIP): a method for 5′- and 3′-genome walking without anchoring

We have devised an improved method of genome walking, named rolling circle amplification of genomic templates for Inverse PCR (RCA–GIP). The method is based on the generation of circular genomic DNA fragments, followed by rolling circle amplification of the circular genomic DNA using ϕ29 DNA polymerase without need for attachment of anchor sequences. In this way from the circular genomic DNA fragments, after RCA amplification, a large amount of linear concatemers is generated suitable for Inverse PCR template that can be amplified, sequenced or cloned allowing the isolation of the 3′- and 5′- of unknown ends of genomic sequences. To prove the concept of the proposed methodology, we used this procedure to isolate the promoter regions from different species. Herein as an example we present the isolation of four promoter regions from Crocus sativus, a crop cultivated for saffron production.     

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

MOTIVATION: Genetic studies focus on increasingly larger genomic regions of both extant and ancient DNA, and there is a need for simulation software to match these technological advances. We present here a new coalescent-based simulation program fastsimcoal, which is able to quickly simulate a variety of genetic markers scattered over very long genomic regions with arbitrary recombination patterns under complex evolutionary scenarios. Availability and Implementation: fastsimcoal is a C++ program compiled for Windows, MacOsX and Linux platforms. It is freely available at cmpg.unibe.ch/software/fastsimcoal/, together with its detailed user manual and example input files.     

A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages

Macroevolutionary trends traditionally are studied by fossil analysis, comparative morphology or evo-devo approaches. With the availability of genome sequences and associated data from an increasing diversity of taxa, it is now possible to add an additional level of analysis: genomic phylostratigraphy. As an example of this approach, we use a phylogenetic framework and embryo expression data from Drosophila to show that grouping genes by their phylogenetic origin can uncover footprints of important adaptive events in evolution.     

bgc: Software for Bayesian estimation of genomic clines

Introgression in admixed populations can be used to identify candidate loci that might underlie adaptation or reproductive isolation. The Bayesian genomic cline model provides a framework for quantifying variable introgression in admixed populations and identifying regions of the genome with extreme introgression that are potentially associated with variation in fitness. Here we describe the bgc software, which uses Markov chain Monte Carlo to estimate the joint posterior probability distribution of the parameters in the Bayesian genomic cline model and designate outlier loci. This software can be used with next‐generation sequence data, accounts for uncertainty in genotypic state, and can incorporate information from linked loci on a genetic map. Output from the analysis is written to an HDF5 file for efficient storage and manipulation. This software is written in C++ . The source code, software manual, compilation instructions and example data sets are available under the GNU Public License at http://sites.google.com/site/bgcsoftware/ .     

Wavelet analysis of DNA walks.

A wavelet transform of the DNA "walk" constructed from a genomic sequence offers a direct visualization of short and long-range patterns in nucleotide sequences. We study sequences that encode diverse biological functions, taken from a variety of genomes. Pattern irregularities in the transform are frequently associated with sequences of biological interest. Exonic regions, for example, visualize differently under wavelet analysis than introns, and ribosomal RNA regions display distinct universal signatures. DNA walk wavelet analysis can provide a sensitive and rapid assessment of the putative biological significance of genomic DNA.     

AGenDA: homology-based gene prediction

We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.     

Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses

Population-based genomic association analyses are more powerful than within-family analyses. However, population stratification (unknown or ignored origin of individuals from multiple source populations) and cryptic relatedness (unknown or ignored covariance between individuals because of their relatedness) are confounding factors in population-based genomic association analyses, which inflate the false-positive rate. As a consequence, false association signals may arise in genomic data association analyses for reasons other than true association between the tested genomic factor (marker genotype, gene or protein expression) and the study phenotype. It is therefore important to correct or account for these confounders in population-based genomic data association analyses. The common correction techniques for population stratification and cryptic relatedness problems are presented here in the phenotype–marker association analysis context, and comments on their suitability for other types of genomic association analyses (for example, phenotype–expression association) are also provided. Even though many of these techniques have originally been developed in the context of human genetics, most of them are also applicable to model organisms and breeding populations.     

Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins

Most dairy cattle populations found in different countries around the world are small to medium sized and use many artificial insemination bulls imported from different foreign countries. The Walloon population in the southern part of Belgium is a good example for such a small-scale population. Wallonia has also a very active community of Holstein breeders requesting high level genetic evaluation services. Single-step Genomic BLUP (ssGBLUP) methods allow the simultaneous use of genomic, pedigree and phenotypic information and could reduce potential biases in the estimation of genomically enhanced breeding values (GEBV). Therefore, in the context of implementing a Walloon genomic evaluation system for Holsteins, it was considered as the best option. However, in contrast to multi-step genomic predictions, natively ssGBLUP will only use local phenotypic information and is unable to use directly important other sources of information coming from abroad, for example Multiple Across Country Evaluation (MACE) results as provided by the Interbull Center (Uppsala, Sweden). Therefore, we developed and implemented single-step Genomic Bayesian Prediction (ssGBayes), as an alternative method for the Walloon genomic evaluations. The ssGBayes method approximated the correct system of equations directly using estimated breeding values (EBV) and associated reliabilities (REL) without any explicit deregression step. In the Walloon genomic evaluation, local information refers to Walloon EBV and REL and foreign information refers to MACE EBV and associated REL. Combining simultaneously all available genotypes, pedigree, local and foreign information in an evaluation can be achieved but adding contributions to left-hand and right-hand sides subtracting double-counted contributions. Correct propagation of external information avoiding double counting of contributions due to relationships and due to records can be achieved. This ssGBayes method computed more accurate predictions for all types of animals. For example, for genotyped animals with low Walloon REL (<0.25) without MACE results but sired by genotyped bulls with MACE results, the average increase of REL for the studied traits was 0.38 points of which 0.08 points could be traced to the inclusion of MACE information. For other categories of genotyped animals, the contribution by MACE information was also high. The Walloon genomic evaluation system passed for the first time the Interbull GEBV tests for several traits in July 2013. Recent experiences reported here refer to its use in April 2016 for the routine genomic evaluations of milk production, udder health and type traits. Results showed that the proposed methodology should also be of interest for other, similar, populations.     

An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals

ABSTRACT: BACKGROUND: The APOBEC3 (A3) genes play a key role in innate antiviral defense in mammals by introducing directed mutations in the DNA. The human genome encodes for seven A3 genes, with multiple splice alternatives. Different A3 proteins display different substrate specificity, but the very basic question on how discerning self from non-self still remains unresolved. Further, the expression of A3 activity/ies shapes the way both viral and host genomes evolve. RESULTS: We present here a detailed temporal analysis of the origin and expansion of the A3 repertoire in mammals. Our data support an evolutionary scenario where the genome of the mammalian ancestor encoded for at least one ancestral A3 gene, and where the genome of the ancestor of placental mammals (and possibly of the ancestor of all mammals) already encoded for an A3Z1-A3Z2-A3Z3 arrangement. Duplication events of the A3 genes have occurred independently in different lineages: humans, cats and horses. In all of them, gene duplication has resulted in changes in enzyme activity and/or substrate specificity, in a paradigmatic example of convergent adaptive evolution at the genomic level. Finally, our results show that evolutionary rates for the three A3Z1, A3Z2 and A3Z3 motifs have significantly decreased in the last 100 Mya. The analysis constitutes a textbook example of the evolution of a gene locus by duplication and sub/neofunctionalization in the context of virus-host arms race. CONCLUSIONS: Our results provide a time framework for identifying ancestral and derived genomic arrangements in the APOBEC loci, and to date the expansion of this gene family for different lineages through time, as a response to changes in viral/retroviral/retrotransposon pressure.     

Optimal spliced alignment of homologous cDNA to a genomic DNA template

MOTIVATION: Supplementary cDNA or EST evidence is often decisive for discriminating between alternative gene predictions derived from computational sequence inspection by any of a number of requisite programs. Without additional experimental effort, this approach must rely on the occurrence of cognate ESTs for the gene under consideration in available, generally incomplete, EST collections for the given species. In some cases, particular exon assignments can be supported by sequence matching even if the cDNA or EST is produced from non-cognate genomic DNA, including different loci of a gene family or homologous loci from different species. However, marginally significant sequence matching alone can also be misleading. We sought to develop an algorithm that would simultaneously score for predicted intrinsic splice site strength and sequence matching between the genomic DNA template and a related cDNA or EST. In this case, weakly predicted splice sites may be chosen for the optimal scoring spliced alignment on the basis of surrounding sequence matching. Strongly predicted splice sites will enter the optimal spliced alignment even without strong sequence matching. RESULTS: We designed a novel algorithm that produces the optimal spliced alignment of a genomic DNA with a cDNA or EST based on scoring for both sequence matching and intrinsic splice site strength. By example, we demonstrate that this combined approach appears to improve gene prediction accuracy compared with current methods that rely only on either search by content and signal or on sequence similarity. AVAILABILITY: The algorithm is available as a C subroutine and is implemented in the SplicePredictor and GeneSeqer programs. The source code is available via anonymous ftp from ftp. zmdb.iastate.edu. Both programs are also implemented as a Web service at http://gremlin1.zool.iastate.edu/cgi-bin/s p.cgiand http://gremlin1.zool.iastate.edu/cgi-bin/g s.cgi, respectively. CONTACT: vbrendel@iastate.edu     

Systematic bias in high-throughput sequencing data and its correction by BEADS

Genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For example, sequencing data of total genomic DNA show significant, yet unexpected enrichments on promoters and exons. This systematic bias is a particular problem for techniques such as chromatin immunoprecipitation, where the signal for a target factor is plotted across genomic features. We have focused on data obtained from Illumina's Genome Analyser platform, where at least three factors contribute to sequence bias: GC content, mappability of sequencing reads, and regional biases that might be generated by local structure. We show that relying on input control as a normalizer is not generally appropriate due to sample to sample variation in bias. To correct sequence bias, we present BEADS (bias elimination algorithm for deep sequencing), a simple three-step normalization scheme that successfully unmasks real binding patterns in ChIP-seq data. We suggest that this procedure be done routinely prior to data interpretation and downstream analyses.