Des confins mozambicains annexés par la puissante Afrique du Sud: Ponto da Ouro

International audiencePonto da Ouro est la dernière localité à l'extrémité sud du littoral mozambicain à proximité de la frontière avec l'Afrique du Sud (fig. 1), au coeur de la région du Maputaland1. Ponto da Ouro est situé aux confins du Mozambique en situation potentielle de fort développement. Sa localisation à proximité de la frontière sudafricaine est excellente et s'intègre dans la logique du développement touristique en corridor entre Richards Bay et Maputo. 117 km de piste sableuse séparent Ponto de Maputo, soit près de 4 heures en 4X4. Environ 350 km séparent Ponto de Richards Bay en Afrique du Sud soit 4 heures de route mais Ponto n'est qu'à quelques kilomètres du grand parc national sud-africain de St Lucia (GSLWP: Greater St Lucia Wetlands Park). Le nom Ponto da Ouro (parfois écrit Ponta d'Ouro) signifie en portugais “ la pointe d'or ” et fait référence à cette pointe rocheuse qui abrite la baie de Ponto (fig. 2 & fig. 3). Cette localité était dans le passé une ville allongée sur plus de 2 kilomètres avec de grandes avenues et un réel front de mer. Aujourd'hui elle donne plutôt l'impression d'une ville sinistrée par la guerre civile. Ce lieu est pourtant incroyablement attachant au carrefour des influences portugaise, mozambicaine et sud-africaine. Pourtant cette dernière influence se fait de plus en plus envahissante

RetrOryza: a database of the rice LTR-retrotransposons

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest

The transforming acidic coiled coil (TACC1) protein modulates the transcriptional activity of the nuclear receptors TR and RAR

Background: The transcriptional activity of Nuclear hormone Receptors (NRs) is regulated by interaction with coactivator or corepressor proteins. Many of these cofactors have been shown to have a misregulated expression or to show a subcellular mislocalization in cancer cell lines or primary tumors. Therefore they can be factors involved in the process of oncogenesis. Results: We describe a novel NR coregulator, TACC1, which belongs to the Transforming Acidic Coiled Coil (TACC) family. The interaction of TACC1 with Thyroid Hormone Receptors (TR) and several other NRs has been shown in a yeast two-hybrid screen and confirmed by GST pulldown, colocalization and co-immunoprecipitation experiments. TACC1 interacts preferentially with unliganded NRs. In F9 cells, endogenous TACC1 localized in the chromatin-enriched fraction of the nucleus and interacted with Retinoid Acid Receptors (RAR alpha) in the nucleus. TACC1 depletion in the cell led to decreased RAR alpha and TR alpha ligand-dependent transcriptional activity and to delocalization of TR from the nucleus to the cytoplasm. Conclusions: From these experimental studies we propose that TACC1 might be a scaffold protein building up a transcriptional complex around the NRs we studied. This function of TACC1 might account for its involvement in several forms of tumour development

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

<p>Abstract</p> <p>Background</p> <p>Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>), induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian <it>X. oryzae </it>pv. <it>oryzicola </it>(<it>Xoc</it>).</p> <p>Results</p> <p>Changes in gene expression of the African <it>Xoo </it>strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH <it>Xoo </it>DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai) with bacteria grown <it>in vitro</it>. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The <it>Xoo </it>MAI1 non-redundant set of sequences was compared against several <it>X. oryzae </it>genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis.</p> <p>Conclusions</p> <p>This is the first report to compare the expression of <it>Xoo </it>genes <it>in planta </it>across different time points during infection. This work shows that as-yet-unidentified and potentially new virulence factors are appearing in an emerging African pathogen. It also confirms that African <it>Xoo </it>strains do differ from their Asian counterparts, even at the transcriptional level.</p

A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

BACKGROUND: Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. RESULTS: Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. CONCLUSIONS: This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c

Large distribution and high sequence identity of a Copia&#8209;type retrotransposon in angiosperm families

International audienceRetrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer