Generalizations of the genomic rank distance to indels

MOTIVATION: The rank distance model represents genome rearrangements in multi-chromosomal genomes as matrix operations, which allows the reconstruction of parsimonious histories of evolution by rearrangements. We seek to generalize this model by allowing for genomes with different gene content, to accommodate a broader range of biological contexts. We approach this generalization by using a matrix representation of genomes. This leads to simple distance formulas and sorting algorithms for genomes with different gene contents, but without duplications. RESULTS: We generalize the rank distance to genomes with different gene content in two different ways. The first approach adds insertions, deletions and the substitution of a single extremity to the basic operations. We show how to efficiently compute this distance. To avoid genomes with incomplete markers, our alternative distance, the rank-indel distance, only uses insertions and deletions of entire chromosomes. We construct phylogenetic trees with our distances and the DCJ-Indel distance for simulated data and real prokaryotic genomes, and compare them against reference trees. For simulated data, our distances outperform the DCJ-Indel distance using the Quartet metric as baseline. This suggests that rank distances are more robust for comparing distantly related species. For real prokaryotic genomes, all rearrangement-based distances yield phylogenetic trees that are topologically distant from the reference (65% similarity with Quartet metric), but are able to cluster related species within their respective clades and distinguish the Shigella strains as the farthest relative of the Escherichia coli strains, a feature not seen in the reference tree. AVAILABILITY AND IMPLEMENTATION: Code and instructions are available at https://github.com/meidanis-lab/rank-indel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

A lower bound on the reversal and transposition diameter

One possible model to study genome evolution is to represent genomes as permutations of genes and compute distances based on the minimum number of certain operations (re-arrangements) needed to transform one permutation into another. Under this model, the shorter the distance, the closer the genomes are. Two operations that have been extensively studied are the reversal and the transposition. A reversal is an operation that reverses the order of the genes on a certain portion of the permutation. A transposition is an operation that 'cuts' a certain portion of the permutation and 'pastes' it elsewhere in the same permutation. In this note, we show that the reversal and transposition distance of the signed permutation pi(n) = (-1 -2... -(n - 1) -n) with respect to the identity is [n/2] +2 for all n greater than or equal to 3. We conjecture that this value is the diameter of the permutation group under these operations.9574374

"Präventivkrieg" als Ausweg? Die USA und der Irak

'In der amerikanischen Irak-Debatte geht es nur vordergründig um den Kampf gegen den Terrorismus. Dieser ist vor allem die innenpolitisch nützliche Legitimation für den Sturz eines nach Massenvernichtungswaffen strebenden Regimes, das als wachsende geopolitische Bedrohung strategischer Interessen in einer kritischen Region gesehen wird. Derzeit verfolgen die USA eine zweigleisige und zugleich zweideutige Politik: Zum einen soll die Eindämmung des Irak durch Sanktionen und Rüstungsinspektionen verstärkt werden, zum anderen werden die militärischen Optionen für einen 'Regimewechsel' vorbereitet. Die Rhetorik ist eindeutig auf den Regimesturz hin orientiert, die militärischen, geheimdienstlichen und politischen Vorbereitungen für eine Intervention und die Zeit danach sind im Gange. Dass die Drohung mit militärischen Optionen in eine politische Lösung - sprich in ein neues Rüstungsüberwachungssystem - münden werde, ist die auf europäischer Seite weithin gehegte Hoffnung. Es ist jedoch sehr fraglich, ob den USA unter Präsident Bush an einer solchen Lösung gelegen wäre. Die Forderung nach neuen Rüstungsinspektionen hat für Teile der Administration in erster Linie die Funktion, die militärische Option zu legitimieren. Kann der massive Einsatz amerikanischer Bodentruppen vermieden und zumindest der Eindruck multilateraler Einbettung erzeugt werden, dann dürften amerikanische Öffentlichkeit und Kongress ein militärisches Vorgehen mit großer Mehrheit unterstützen. Noch sind führende Politiker im Kongress jedoch nicht der Auffassung, dass der Irak eine unmittelbare, ein baldiges militärisches Vorgehen rechtfertigende Bedrohung darstellt. Präsident Bush mag aus Gründen des dauerhaften politischen Rückhalts gut beraten sein, vor einem Krieg gegen den Irak die Zustimmung des Kongresses einzuholen. Erzwingen wird der Kongress seine Mitsprache jedoch nicht. Ungewiss ist, ob der Präsident am Ende vor der vollen Konsequenz eines militärischen Vorgehens - nämlich Besetzung und Restrukturierung des politischen Systems des Irak - aufgrund der politischen und strategischen Risiken und Kosten zurückschreckt. Staatsmänner sind jedoch mitunter zu äußerst riskanten Schritten bereit, wenn die künftige Bedrohung als so groß gewertet wird, dass ein Krieg als das geringere Risiko eingeschätzt wird, oder wenn am Ende einer erfolglosen Drohpolitik die eigene Glaubwürdigkeit und die der Nation auf dem Spiel zu stehen scheint. Ein ohne Mandat der Vereinten Nationen geführter Präventivkrieg gegen den Irak, um dessen Regime zu stürzen, wäre eine völkerrechtlich, politisch und ethisch höchst problematische Entwicklung: völkerrechtlich, weil die Beschränkungen für den Einsatz militärischer Macht gelockert würden; politisch, weil es sich um einen Präzedenzfall handeln würde, auf den sich andere berufen könnten; ethisch, weil sich ein präemptives militärisches Handeln nur angesichts eines drohenden Krieges rechtfertigen lässt - wenn der Verzicht auf Präemption eine ernsthafte Gefährdung für die territoriale Integrität und politische Unabhängigkeit eines Staates darstellen würde. So wünschenswert ein Ende der Diktatur im Irak wäre - die Entscheidung zu einem Krieg birgt so viele völkerrechtliche, ethische und strategische Probleme, dass die Alternative, nämlich eine robuste Eindämmungspolitik, nicht vorschnell als aussichtslos und zu riskant verworfen werden sollte. Gerade die Einschätzung, dass die USA auf einen militärischen Angriff gegen den Irak zusteuern, hat eine veränderte Konstellation geschaffen, die von europäischer Seite für eine Verstärkung der Eindämmungspolitik genutzt werden könnte.' (Autorenreferat

Xylella fastidiosa gene expression analysis by DNA microarrays

Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition

Evolution of an endofungal Lifestyle: Deductions from the Burkholderia rhizoxinica Genome

<p>Abstract</p> <p>Background</p> <p><it>Burkholderia rhizoxinica </it>is an intracellular symbiont of the phytopathogenic zygomycete <it>Rhizopus microsporus</it>, the causative agent of rice seedling blight. The endosymbiont produces the antimitotic macrolide rhizoxin for its host. It is vertically transmitted within vegetative spores and is essential for spore formation of the fungus. To shed light on the evolution and genetic potential of this model organism, we analysed the whole genome of <it>B. rhizoxinica </it>HKI 0454 - a type strain of endofungal <it>Burkholderia </it>species.</p> <p>Results</p> <p>The genome consists of a structurally conserved chromosome and two plasmids. Compared to free-living <it>Burkholderia </it>species, the genome is smaller in size and harbors less transcriptional regulator genes. Instead, we observed accumulation of transposons over the genome. Prediction of primary metabolic pathways and transporters suggests that endosymbionts consume host metabolites like citrate, but might deliver some amino acids and cofactors to the host. The rhizoxin biosynthesis gene cluster shows evolutionary traces of horizontal gene transfer. Furthermore, we analysed gene clusters coding for nonribosomal peptide synthetases (NRPS). Notably, <it>B. rhizoxinica </it>lacks common genes which are dedicated to quorum sensing systems, but is equipped with a large number of virulence-related factors and putative type III effectors.</p> <p>Conclusions</p> <p><it>B. rhizoxinica </it>is the first endofungal bacterium, whose genome has been sequenced. Here, we present models of evolution, metabolism and tools for host-symbiont interaction of the endofungal bacterium deduced from whole genome analyses. Genome size and structure suggest that <it>B. rhizoxinica </it>is in an early phase of adaptation to the intracellular lifestyle (genome in transition). By analysis of tranporters and metabolic pathways we predict how metabolites might be exchanged between the symbiont and its host. Gene clusters for biosynthesis of secondary metabolites represent novel targets for genomic mining of cryptic natural products. <it>In silico </it>analyses of virulence-associated genes, secreted proteins and effectors might inspire future studies on molecular mechanisms underlying bacterial-fungal interaction.</p

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica