The where and wherefore of evolutionary breakpoints

The 'action' in genome-level evolution lies not in the large gene-containing segments that are conserved among related species, but in the breakpoint regions between these segments. Two recent papers in BMC Genomics detail the pattern of repetitive elements associated with breakpoints and the epigenetic conditions under which breakage occurs

Median inverse problem and approximating the number of kk-median inverses of a permutation

We introduce the "Median Inverse Problem" for metric spaces. In particular, having a permutation $\pi$ in the symmetric group $S_n$ (endowed with the breakpoint distance), we study the set of all $k$-subsets $\{x_1,...,x_k\}\subset S_n$ for which $\pi$ is a breakpoint median. The set of all $k$-tuples $(x_1,...,x_k)$ with this property is called the $k$-median inverse of $\pi$. Finding an upper bound for the cardinality of this set, we provide an asymptotic upper bound for the probability that $\pi$ is a breakpoint median of $k$ permutations $\xi_1^{(n)},...,\xi_k^{(n)}$ chosen uniformly and independently at random from $S_n$

Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes

BACKGROUND: Ancestral gene order reconstruction for flowering plants has lagged behind developments in yeasts, insects and higher animals, because of the recency of widespread plant genome sequencing, sequencers' embargoes on public data use, paralogies due to whole genome duplication (WGD) and fractionation of undeleted duplicates, extensive paralogy from other sources, and the computational cost of existing methods. RESULTS: We address these problems, using the gene order of four core eudicot genomes (cacao, castor bean, papaya and grapevine) that have escaped any recent WGD events, and two others (poplar and cucumber) that descend from independent WGDs, in inferring the ancestral gene order of the rosid clade and those of its main subgroups, the fabids and malvids. We improve and adapt techniques including the OMG method for extracting large, paralogy-free, multiple orthologies from conflated pairwise synteny data among the six genomes and the PATHGROUPS approach for ancestral gene order reconstruction in a given phylogeny, where some genomes may be descendants of WGD events. We use the gene order evidence to evaluate the hypothesis that the order Malpighiales belongs to the malvids rather than as traditionally assigned to the fabids. CONCLUSIONS: Gene orders of ancestral eudicot species, involving 10,000 or more genes can be reconstructed in an efficient, parsimonious and consistent way, despite paralogies due to WGD and other processes. Pairwise genomic syntenies provide appropriate input to a parameter-free procedure of multiple ortholog identification followed by gene-order reconstruction in solving instances of the "small phylogeny" problem

Un modèle pour l’alternance de langue sous la contrainte d’équivalence

Comment peut-on combiner les grammaires de deux langues afin de construire un modèle du comportement des bilingues? Plus spécifiquement, est-ce possible de trouver un modèle de l’alternance de langue qui est soumise à la contrainte d’équivalence sur l’ordre des mots? Nous répondons à cette question au niveau formel, en nous servant de grammaires indépendantes du contexte qui rendent compte du comportement unilingue et du comportement bilingue. Notre solution satisfait à plusieurs conditions qui portent sur l’identification de la langue à assigner aux constituants de la phrase. Nous montrons comment adapter la théorie des grammaires probabilistes à la prédiction de la fréquence de points d’alternance possibles dans une situation donnée de bilinguisme et nous l’appliquons à quelques paires de langues qui diffèrent entre elles par rapport à l’ordre des mots.Given the grammars of two langues, how can we combine them to model bilingual behaviour such as code-switching under the equivalence constraint on word-order? We answer this question on the formal level, making use of context-free grammars for both unilingual and bilingual behaviour. Our solution satisfies a number of conditions on the language assigned (if any) to higher-order constituents in the phrase-structure. We show how to adapt the theory of probabilistic grammars to the prediction of switch-point abundance for a given bilingual situation and we apply this to a number of language pairs exhibiting diverse word-order contrasts

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution

BACKGROUND: We study the relation between genome rearrangements, breakpoints and gene expression. Genome rearrangement research has been concerned with the creation of breakpoints and their position in the chromosome, but the functional consequences of individual breakpoints remain virtually unknown, and there are no direct genome-wide studies of breakpoints from this point of view. A question arises of what the biological consequences of breakpoint creation are, rather than just their structural aspects. The question is whether proximity to the site of a breakpoint event changes the activity of a gene. RESULTS: We investigate this by comparing the distribution of distances to the nearest breakpoint of genes that are differentially expressed with the distribution of the same distances for the entire gene complement. We study this in data on whole blood tissue in human versus macaque, and in cerebral cortex tissue in human versus chimpanzee. We find in both data sets that the distribution of distances to the nearest breakpoint of "changed expression genes" differs little from this distance calculated for the rest of the gene complement. In focusing on the changed expression genes closest to the breakpoints, however, we discover that several of these have previously been implicated in the literature as being connected to the evolutionary divergence of humans from other primates. CONCLUSIONS: We conjecture that chromosomal rearrangements occasionally interrupt the regulatory configurations of genes close to the breakpoint, leading to changes in expression