Virus evolution : the emergence of new ideas (and re-emergence of old ones)

Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms appearing daily in the H5N1 avian flu virus [1], than to the fundamental interrogation: where do viruses come from? This situation is now rapidly changing, due to the coincidence of bold new ideas (and sometimes the revival of old ones), the unexpected features exhibited by recently isolated spectacular viruses [2] (see at URL: www.giantvirus.org), as well as the steady increase of genomic sequences for 'regular' viruses and cellular organisms enhancing the power of comparative genomics [3]. After being considered non-living and relegated in the wings by a majority of biologists, viruses are now pushed back on the center stage: they might have been at the origin of DNA, of the eukaryotic cell, and even of today's partition of biological organisms into 3 domains of life: bacteria, archaea and eukarya. Here, I quickly survey some of the recent discoveries and the new evolutionary thoughts they have prompted, before adding to the confusion with one interrogation of my own: what if we totally missed the true nature of (at least some) viruses?Comment: submitte

Mimivirus Relatives in the Sargasso Sea

The discovery and genome analysis of Acanthamoeba polyphaga Mimivirus, the largest known DNA virus, challenged much of the accepted dogma regarding viruses. Its particle size (>400 nm), genome length (1.2 million bp) and huge gene repertoire (911 protein coding genes) all contribute to blur the established boundaries between viruses and the smallest parasitic cellular organisms. Phylogenetic analyses also suggested that the Mimivirus lineage could have emerged prior to the individualization of cellular organisms from the three established domains, triggering a debate that can only be resolved by generating and analyzing more data. The next step is then to seek some evidence that Mimivirus is not the only representative of its kind and determine where to look for new Mimiviridae. An exhaustive similarity search of all Mimivirus predicted proteins against all publicly available sequences identified many of their closest homologues among the Sargasso Sea environmental sequences. Subsequent phylogenetic analyses suggested that unknown large viruses evolutionarily closer to Mimivirus than to any presently characterized species exist in abundance in the Sargasso Sea. Their isolation and genome sequencing could prove invaluable in understanding the origin and diversity of large DNA viruses, and shed some light on the role they eventually played in the emergence of eukaryotes.Comment: see also http://www.giantvirus.or

Major results and research challenges in cotton molecular genetics at Cirad (France)

CIRAD (Montpellier, France) develops research activities centered on tropical and sub-tropical agricultural systems. Among others crops, cotton is the fucus of a series of research programs in different disciplines from economics to breeding. Major areas in genetics and breeding relate to (1) genetic diversity, (2) cultivar development through classical and molecular breeding, and (3) applied genomics. An important but under-exploited reservoir of genetic diversity exists within the genus Gossypium. With over 3000 accessions CIRAD has one of the few important gene banks worldwide. It includes cultivars, landraces , and wild Gossypiurn species. DNA molecular markeTs have shawn their usefulness and validity for fingerprinting plant resources and for structuring diversity of large collections. In our case, after a preliminary step centered on the screening of microsatellite markers over a limited set of accessions of the gene bank (a genotyping kit has been proposed) , our future plans include the use of high-throughput methods of genotyping (a DArT platform will soon be available in our unit). Opportunities for exploiting this large diversity relate to the development core-collections and of genetic association studies for a given set of traits (fiber quality, stress response) . After a past and fruitful period of collaboration in different tropical countries (varieties co-obtained by ClRAD are cultivated on over 2. 5 million hectares worldwide), CIRAD has more recently engaged research programs in molecular genetics. Focus has initially been on fiber quality as a target trait and on markerassisted interspecific breeding for introgressing fiber quality traits from G. barbadense into G. hirsutUtn. Achievements in this area (genetic maps, fiber quality QTLs) have been published and are posted on the web. The database of CIRAD, TropGene DB (available at http, lltropgenedb. cirad. h l ) is regularly updated and presently displays various genetic maps as well as QTL data. Based upon QTL detected in the BCI and BC2 (backcross to the Gh parent) generations, marker-assisted selection in further generations (BC3 to BCG) was conducted and advanced lines introgressed with 3 ~ 5 QTLs were tested under tropical conditions. Using the same material, libraries of segmental introgression lines are being created for a few specifie target chromosomes. More recently , through collaboration with Embrapa (Brazil), CIRAD has initiated research on disease and nematode resistances in order to clarify the genetic basis of resistance; prepare segregating populations, and develop marker-assisted selection programs. A new collaborative project coordinated by CIRAD on the genetics and genomics of cotton fiber quality has been launched in 2007. CIRAD and its partners, Bayer CS and CSIRü, are engaged in ambitious research aimed at elucidating the genetic basis of fiber quality. The project is centered on an interspecific RIL population (a cross between 2 weil studied parents , Guazuncho 2 (G. hirsuturn) and VH8 (G. harhadense)) . It is innovative by the approach combining (1) phenotypic assessment of fi ber quality from field and greenhouse experiments on four continents, and (2) transcriptome profiling using complementary platforms, hybridization-based (microarrays) and PCR-based (cDNA-AFLP). Comparison of QTL and eQTL results is expected to help in identifying candidate genes important in fiber quality. (Résumé d'auteur

Clusterisation du Web en vue d'extraction de corpus homogènes

ISBN 2-906855-18-9Web resources are more and more different, not only regarding thematic content but also related to type of document, geographic origin, level, language, etc. However, web search engines do not take into account this heterogeneity and propose only a thematic access by keywords to the documents. This paper presents a method allowing to extract homogenous corpus of web documents. This method based on link analysis uses co-citation method and focuses more specially on the notion of type of web documents.Les ressources disponibles sur le Web sont de plus en plus diverses aussi bien d'un point de vue thématique, qu'au niveau de leur type, de leur origine géographique, etc. Cependant, les outils de recherche ne prennent pas en compte cette hétérogénéité et ne proposent qu'un accès par mots-clés aux documents du web. Cet article présente une méthode basée sur les hyperliens, permettant d'extraire du graphe Web des sous-corpus de documents homogènes. L'expérience décrite ici utilise la méthode des co-citations et s'intéresse plus spécialement à la notion de genre (type) de document web

Propagation de métadonnées par l'analyse des liens

http://www.emse.fr/~mbeig/PUBLIS/2003-jft-p257-prime.pdfInternational audienc

Non-independence between markers on homoeologous chromosomes in an interspecific allopolyploid cotton RILs population

Cotton, as the world's main natural textile fibre, is the focus of many studies for genetic improvement of fibre quality. Two allotetraploid (AtDt genome, 2n=4X=52) species dominate world production: G. hirsutum (Gh) with medium fibre quality and G. barbadense (Gb) with high fibre quality, accounting for 95% / 3% of production respectively. A RIL population originating from a Gh-Gb cross is the base material of the CIRAD-Bayer CropScience-CSIRO ANR research project Cotton_RILs, aiming at the genetic and genomic dissection of cotton fibre quality for introgression of high fibre quality genes of Gb into Gh germplasm. Until now, classical breeding did not succeed at satisfactorily combining traits from both cotton species, in spite of high apparent synteny conservation between their chromosomes. The fixed heterozygosity of allopolyploids is supposed to result in gene expression changes, or expression subfonctionalization, a partitioning of the ancestral expression domains among duplicate genes. It is hypothesized that allopolyploids should be subject to more genetic and epigenetic regulatory changes than autopolyploids. We report here on evidence of interactions between markers on pairs of homoeologous chromosomes in the Gh-Gb RIL population studied (140 lines genotyped with 800 markers, assembled in a saturated map of 26 linkage groups). In five of the 13 homoeologous chromosome pairs (c12-c26, c6-c25, c11-c21, c3-c17 and c13-c18), markers from homoeologs displayed unexpectedly high linkage (LOD from 9 to 14). Such linkage was not observed between chromosomes from non-homoeologous pairs. The association concerns 1-3 markers from one chromosome against stretches of 5-8 or more markers on the homoeolog. Gametic disequilibrium (GD) has been assessed pairwise between all markers. Positive GD is highly dominant between markers of homoeologous chromosomes, but negative as well as positive GD are observed between markers of non-homoeologs, with uneven distribution. In positive GD, frequencies of Gh-Gb allelic combinations are very low, meanwhile in negative GD, there is uniform low frequency of Gb-Gb allelic combinations. Diverse genetic and epigenetic mechanisms have been characterized in polyploid plants, including unequal expression of duplicate genes, segregation distortion and restricted recombination; in cotton, lesser retention of Gb alleles is a common feature of advancedgeneration backcross or RIL interspecific populations. Our results support hypotheses of intergenomic incompatibility, with selection during inbreeding that favoured elimination of Gh-Gb allelic combinations that were too conflicting regarding the expression of duplicate genes. (Texte intégral

The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

International audienceBackground: Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results: We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions: In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups

mRNA maturation in giant viruses: variation on a theme

International audienceGiant viruses from the Mimiviridae family replicate entirely in their host cytoplasm where their genes are transcribed by a viral transcription apparatus. mRNA polyadenylation uniquely occurs at hairpin-forming palindromic sequences terminating viral transcripts. Here we show that a conserved gene cluster both encode the enzyme responsible for the hairpin cleavage and the viral polyA polymerases (vPAP). Unexpectedly, the vPAPs are homodimeric and uniquely self-processive. The vPAP backbone structures exhibit a symmetrical architecture with two subdomains sharing a nucleotidyltransferase topology, suggesting that vPAPs originate from an ancestral duplication. A Poxvirus processivity factor homologue encoded by Megavirus chilensis displays a conserved 5'-GpppA 2'O methyltransferase activity but is also able to internally methylate the mRNAs' polyA tails. These findings elucidate how the arm wrestling between hosts and their viruses to access the translation machinery is taking place in Mimiviridae

Draft genome sequence of an alphaproteobacterium associated with the Mediterranean sponge Oscarella lobularis

While sequencing DNA purified from the homoscleromorph sponge Oscarella lobularis, we detected a large number of reads with strong similarity to available alphaproteobacteria gene sequences of family Rhodobacteraceae. Here, we present the genome sequence of this putative sponge symbiont that we propose to designate as “Candidatus Rhodobacter lobularis.” (Résumé d'auteur