H. Quesneville

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one m...

We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype (ARK), structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassiceceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. Based on these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, 'DicotSyntenyViewer' (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.

summary The proportions of aected sibs sharing 2, 1 or 0 identical by descent parental marker alleles have been shown to conform to the 'triangle constraints' (Suarez, 1978; Holmans, 1993). It has also been shown (Dudoit & Speed, 1999) that the constraints are verified provided certain assumptions hold. In this study we explore a realistic situation in which the constraints

... Sharadha Sakthikumarb, Asaf A. Salamovd, Jeremy Schmutzd, Benjamin Sellesa, Harris Shapirod, Philippe Tanguaye, Gerald A. Tuskand,l, Bernard Henrissatg, Yves Van de Peerc, Pierre Rouzéc, Jeffrey G. Ellisj, Peter N. Doddsj, Jacqueline E. Scheinh ... Duplessis et al. Page 3. ...

For any genetic model, Holmans showed that the proportions of affected sibs sharing 2, 1, or 0 identical-by-descent parental marker alleles are constrained to belong to a specific triangle. The triangle constraints do not hold when the sib phenotypes are determined by different models. We test the rejection of triangle constraints on affected sib pairs discordant for severity, to determine whether different models control the severe and mild forms of the disease in the simulated data. With this method we show that a locus on chromosome 5 plays a different role in the two forms of the disease.

The proportions of affected sibs sharing 2, 1 or 0 identical by descent parental marker alleles have been shown to conform to the 'triangle constraints' (Suarez, 1978; Holmans, 1993). It has also been shown (Dudoit & Speed, 1999) that the constraints are verified provided certain assumptions hold. In this study we explore a realistic situation in which the constraints fail due to the presence of a factor in which the sibs differ, a factor on which penetrance depends. This factor may be a characteristic of the trait (severe vs. mild form), or the presence/absence of an associated trait or an environmental factor. We show that under such situations, using the triangle constraints may lead to important loss of power to detect linkage by the MLS test. We propose here an alternative approach in order to detect both linkage and heterogeneity.

ABSTRACT We studied transposable elements (TEs) impact on gene transcription using high-throughput sequencing (RNA-Seq). TEs, which turn out to be expressed in euchromatin as well as in heterochromatin, interact with genes at different levels. First, active TEs seem to accumulate in the 5' upstream regions of the genes, possibly providing an alternative transcript of the nearby gene. Indeed, in some cases, the TE transcript is co-linear and overlapping to the gene. Second, apart from the 5' upstream regions, most active TEs seem transcribed on the same strand as the gene. Conversely, few anti-sense-TEs with respect to the gene are observed. This suggests that anti-sense TEs insertions have a disruptive action and are counter-selected. The only exceptions are when the TEs are located in introns, where they could provide another complex way of regulating the gene, and in the 3' downstream region, where other mechanisms akin to siRNAs could take place. Third, we noted several cases where a non-canonical transcriptional start site (TSS) is present on the TE. This cryptic-TSS is located on specific TE fragments that appear to be selected among other TE fragments when close to genes. All together, these results suggest that the active transposable elements influence the transcription in the host genome. It is likely that some features of transposable elements have been exaptated in order to enrich some genes, and possibly acquire new functions.