Mutator system derivatives isolated from sugarcane genome sequence

Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I- IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/ Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. (Résumé d'auteur

Production of new interspecific cotton (Gossypium spp.) hybrids highly resistant to the reniform nematode (Rotylenchulus reniformis).

peer reviewe

Highlighting the occurrence of tetraploidy in Acacia senegal (L.) Willd. and genetic variation patterns in its natural range revealed by DNA microsatellite markers

Acacia senegal (L.) Willd. is the main species producing the internationally traded gum arabic. Genetic studies of this species are rare and until now the chromosome number was thought to be diploid (2n = 2x = 26). Here, using chromosome number counting, we demonstrate for the first time that tetraploids (2n = 4x = 52) also occur in A. senegal. Nuclear and chloroplast microsatellite markers were used to estimate and compare genetic variation within this newly described polyploidy complex in the Sudano-Sahelian region in Africa. Genetic diversity was higher in diploids, suggesting that the formation of tetraploids is recent and that mutation-drift equilibrium has not yet been reached. The two cytotypes do not have the same genetic structure and are genetically differentiated. Among tetraploids, populations are greatly differentiated and do not share the same chlorotypes. Based on these results, we discuss recurrent formation of tetraploids from different diploid progenitors across the distribution range of A. senegal in the Sudano-Sahelian zone

Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis)

P>Enriched genomic libraries in GA and GT tandem repeat motifs were generated from rubber tree (Hevea brasiliensis). Design of appropriate primer pairs in the flanking regions enables to produce amplified fragments for 310 of these sequences. The test of these genomic microsatellites on a set of 10 rubber tree genotypes allows the characterization of 296 new polymorphic markers. Expected heterozygosity ranged from 0.10 to 0.93 and allele numbers from 2 to 11. Microsatellite loci with GA motifs were more abundant, longer and more polymorphic than GT motifs. Such a high variability suggests the utility of these markers for the establishment of integrated linkage maps, as well as the characterization of linkage disequilibrium in rubber tree populations.1302294296French government (SCSP-Cirad)Genoscope (Evry, France

Radiation of the Nod-independent Aeschynomene relies on multiple allopolyploid speciation events

The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A.indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. These analyses demonstrate the existence of an A.indica polyploid species complex comprising A.evenia (C. Wright) (2n=2x=20), A.indica L. s.s. (2n=4x=40) and a new hexaploid form (2n=6x=60). This latter contains the two genomes present in the tetraploid (A.evenia and A.scabra) and another unidentified genome. Two other species, A.pratensis and A.virginica, are also shown to be of allopolyploid origin. This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene

An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

Premise of the study : In this study, we developed a nuclear DNA extraction protocol for Next Generation Sequencers (NGS). Methods and Results : We applied this extraction method to grapevines and coffee trees, which are known to contain many secondary metabolites. The nuclear DNA obtained was sequenced by the 454/GS-FLX method. We obtained excellent results, with less than 4% cytoplasmic DNA, in a similar way to a BAC (Bacterial Artificial Chromosome)-building protocol. We also compared our protocol with a classic DNA extraction using specific cytoplasmic DNA amplification. Results showed a lower cytoplasmic DNA contamination with the new protocol. Conclusions : The method presented here is fast and economical. The DNA obtained is of high quality, with a low level of cytoplasmic DNA contamination, and very efficient for the construction of sequencing libraries