A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond

<p>Abstract</p> <p>Background</p> <p>The role of gene duplication in the structural and functional evolution of genomes has been well documented. Analysis of complete rice (<it>Oryza sativa</it>) genome sequences suggested an ancient whole genome duplication, common to all the grasses, some 50-70 million years ago and a more conserved segmental duplication between the distal regions of the short arms of chromosomes 11 and 12, whose evolutionary history is controversial.</p> <p>Results</p> <p>We have carried out a comparative analysis of this duplication within the wild species of the genus <it>Oryza</it>, using a phylogenetic approach to specify its origin and evolutionary dynamics. Paralogous pairs were isolated for nine genes selected throughout the region in all <it>Oryza </it>genome types, as well as in two outgroup species, <it>Leersia perrieri </it>and <it>Potamophila parviflora</it>. All <it>Oryza </it>species display the same global evolutionary dynamics but some lineage-specific features appear towards the proximal end of the duplicated region. The same level of conservation is observed between the redundant copies of the tetraploid species <it>Oryza minuta</it>. The presence of orthologous duplicated blocks in the genome of the more distantly-related species, <it>Brachypodium distachyon</it>, strongly suggests that this duplication between chromosomes 11 and 12 was formed as part of the whole genome duplication common to all Poaceae.</p> <p>Conclusion</p> <p>Our observations suggest that recurrent but heterogeneous concerted evolution throughout the <it>Oryza </it>genus and in related species has led specifically to the extremely high sequence conservation occurring in this region of more than 2 Mbp.</p

The m 6 A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

International audienceGlobal, segmental, and gene duplication-related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m 6 A)-assisted polyadenylation (m-ASP) pathway ensures tran-scriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m 6 A methyltransferase-associated factor FIP37 and CPSF30L, an m 6 A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37-and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 39-UTR m 6 A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants

Evolution of a relationship: how Ostreococcus tauri viruses circumvent host resistance

Marine microeukaryotes battle every day with environmental pressures, predators and viruses to survive. To escape and survive certain threats they often have to change their life cycle stage for the cost of a lower growth rate. Marine viruses are ubiquitous in the oceans but they are unable to replicate without infecting host cells. Therefore they have to evolve as quickly as their host and change their infection strategy. Spontaneous resistance of the green microalgae Ostreococcus tauri occurs in culture once it is infected with the virus OtV5. Two newly isolated viruses were able to lyse these OtV5-resistant O. tauri cells. While o could only lyse OtV5-resistant cells, OtV15 was able to lyse both OtV5-susceptible and –resistant cells. Similar as the O. lucimarinus viruses, their genomes have a high level of synteny with 182 orthologous genes, reduced to 173 when including OtV1 and OtV2. We will discuss potential infection strategies based upon their specific genes. High-throughput sequencing projects like the Ocean Sampling Day and Tara Oceans Expedition enable us to monitor O. tauri and its viruses around the world

The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana

International audienceArginine/R methylation (R-met) of proteins is a widespread post-translational modification (PTM), deposited by a family of protein arginine/R methyl transferase enzymes (PRMT). Regulations by R-met are involved in key biological processes deeply studied in metazoan. Among those, post-transcriptional gene silencing (PTGS) can be regulated by R-met in animals and in plants. It mainly contributes to safeguard processes as protection of genome integrity in germlines through the regulation of piRNA pathway in metazoan, or response to bacterial infection through the control of AGO2 in plants. So far, only PRMT5 has been identified as the AGO/PIWI R-met writer in higher eukaryotes. We uncovered that AGO1, the main PTGS effector regulating plant development, contains unique R-met features among the AGO/PIWI superfamily, and outstanding in eukaryotes. Indeed, AGO1 contains both symmetric (sDMA) and asymmetric (aDMA) R-dimethylations and is dually targeted by PRMT5 and by another type I PRMT in Arabidopsis thaliana. We showed also that loss of sDMA didn’t compromise AtAGO1 subcellular trafficking in planta. Interestingly, we underscored that AtPRMT5 specifically promotes the loading of phasiRNA in AtAGO1. All our observations bring to consider this dual regulation of AtAGO1 in plant development and response to environment, and pinpoint the complexity of AGO1 post-translational regulation

Evidence for ARGONAUTE4–DNA interactions in RNA-directed DNA methylation in plants

International audienc