Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing

[EN] Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplastreplicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear potato spindle tuber viroid (PSTVd, Pospiviroidae). This revealed higher mutation frequencies in ELVd than in PSTVd, as well as marked differences in the types of mutations produced. Rates of spontaneous mutation, quantified in vivo using the lethal mutation method, ranged from 1/1000 to 1/800 for ELVd and from 1/7000 to 1/3800 for PSTVd depending on sequencing run. These results suggest that extremely high mutability is a common feature of chloroplastic viroids, whereas the mutation rates of PSTVd and potentially other nuclear viroids appear significantly lower and closer to those of some RNA viruses.This work was supported by the European Research Council (erc.europa.eu; ERC-2011-StG-281191-VIRMUT to RS), the Spanish Ministerio de Economia y Competitividad (www.mineco.gob.es; BFU2013-41329 grant to RS, BFU2014-56812-P grant to RF, and a predoctoral fellowship to ALC), and the Spanish Junta de Comunidades de Castilla-La Mancha (www.castillalamancha.es;postdoctoral fellowship to CB). 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Investigació i gènere a la Universitat Jaume I 2016

Actes del II Congrès d’Investigació i Gènere a la Universitat Jaume I, celebrat l’11 de maig de 2016 a la Universitat Jaume I.La igualtat de dones i homes, tot i ser un principi jurídic universal recollit en normes internacionals i nacionals i que es troba en la base dels sistemes democràtics, és difícil d'aconseguir. Per això hi ha un consens generalitzat sobre la necessitat d'impulsar actuacions transversals i accions positives en tots els àmbits. És en aquest context en el qual van sorgir, entre altres mesures, l'obligatorietat legal de crear plans d'igualtat en organitzacions amb més de 250 treballadors (Llei orgànica 3/2007 per a la igualtat efectiva de dones i homes) i en el cas concret de les universitats espanyoles, de considerar-les part de la seua estructura d'organització segons s'estableix en la disposició addicional dotzena de la Llei orgànica 4/2007, de 12 d'abril, d'universitats. La Universitat Jaume I presenta en aquesta publicació les actes del II Congrés d’Investigació i Gènere que van tenir lloc a l'UJI i que inclouen treballs de final de grau i de màster, tesis doctorals, projectes d'investigació i activitat docent de grau

Viroids: the minimal non-coding RNAs with autonomous replication

[EN] Viroids are small (246¿401 nucleotides), non-coding, circular RNAs able to replicate autonomously in certain plants. Viroids are classified into the families Pospiviroidae and Avsunviroidae, whose members replicate in the nucleus and chloroplast, respectively. Replication occurs by an RNA-based rolling-circle mechanism in three steps: (1) synthesis of longerthan-unit strands catalyzed by host DNA-dependent RNA polymerases forced to transcribe RNA templates, (2) processing to unit-length, which in family Avsunviroidae is mediated by hammerhead ribozymes, and (3) circularization either through an RNA ligase or autocatalytically. Disease induction might result from the accumulation of viroid-specific small interfering RNAs that, via RNA silencing, could interfere with normal developmental pathways.This work was partially supported by grants from the Ministerio de Ciencia y Tecnologia (BMC2002-03694) and from the Generalidad Valenciana (Spain).Flores Pedauye, R.; Delgado Villar, SG.; Gas, M.; Carbonell, A.; Molina, D.; Gago, S.; La Peña Del Rivero, MD. (2004). Viroids: the minimal non-coding RNAs with autonomous replication. FEBS Letters. 567(1):42-48. https://doi.org/10.1016/j.febslet.2004.03.1184248567

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

International audienceAbstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e . the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene