An RNA Virome Associated to the Golden Orb-Weaver Spider Nephila clavipes

The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey.CIAP Instituto de Patologia VegetalFil: Debat,Humberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentin

A South American Mouse Morbillivirus Provides Insight into a Clade of Rodent-Borne Morbilliviruses

Morbilliviruses are negative-sense single-stranded monosegmented RNA viruses in the family Paramyxoviridae (order Mononegavirales). Morbilliviruses infect diverse mammals including humans, dogs, cats, small ruminants, seals, and cetaceans, which serve as natural hosts. Here, I report the identification and characterization of novel viruses detected in public RNAseq datasets of South American long-haired and olive field mice. The divergent viruses dubbed Ratón oliváceo morbillivirus (RoMV) detected in renal samples from mice collected from Chile and Argentina are characterized by an unusually large genome including long intergenic regions and the presence of an accessory protein between the F and H genes redounding in a genome architecture consisting in 3′-N-P/V/C-M-F-hp-H-L-5′. Structural and functional annotation, genetic distance, and evolutionary insights suggest that RoMV is a member of a novel species within genus Morbillivirus tentatively named as South American mouse morbillivirus. Phylogenetic analysis suggests that this mouse morbillivirus is closely related to and clusters into a monophyletic group of novel rodent-borne morbilliviruses. This subclade of divergent viruses expands the host range, redefines the genomic organization and provides insights on the evolutionary history of genus Morbillivirus.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin

Dataset of the transcribed 45S ribosomal RNA sequence of the tree crop yerba mate

This contribution contains data related to the research article entitled The 18S-25S ribosomal RNA unit of yerba mate (Ilex paraguariensis A. St.-Hil.) (Aguilera et al., 2016). Through a bioinformatic approach involving NGS data, we provide information of the transcribed 45S ribosomal RNA (rRNA) sequence of yerba mate, the first reference for the Ilex L. genus. This dataset comprises information regarding the assembly and annotation of this rRNA unit. The generated data is applicable for comparative analysis and evolutionary studies among Ilex and related taxa. The raw sequencing data used here is available at DDBJ/EMBL/GenBank (NCBI Resource Coordinators, 2016) Sequence Read Archive (SRA) under the accession SRP043293 and the consensus 45S ribosomal RNA sequence has been deposited there under the accession GFHV00000000.Fil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentin

Plan S in Latin America: a precautionary note

Background: Latin America has historically led a vital and open access movement andleads the worldwide region with the adoption of wider open access practices. Argentina has expressed its commitment to join Plan S, an initiative from a European consortiumof research funders with a mandate to promote the open access publishing of scientific outputs. Analysis: This opinion article suggests that the potential adhesion of Argentina orother Latin American nations to Plan S ignores the reality and tradition of Latin American open access publishing. Conclusion and implications: Plan S must demonstrate that it will encourage at aregional and global level the advancement of non-commercial open access initiatives.Latin America should invest and promote open nonprofit scholarly-led infrastructures, allowing the academy to regain control of scholarly communications.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFYMA); ArgentinaFil: Babini, Dominique. Consejo Latinoamericano de Ciencias Sociales (CLACSO). Argentin

El Paisaje Actual de Publicaciones Académicas: una Visión Emergente desde el Sur Global

Una gran parte del sistema de publicaciones académicas tradicional es desigual, poco confiable, excluyente, discriminatorio, sesgado, depredador, insostenible y opaco [1]. Aproximadamente el 70 % de los artículos de revistas científicas están detrás de muros de pago [2, 3], lo que despoja a la población de información vital y obstaculiza el progreso de la investigación científica. La industria editorial ha secuestrado y mercantilizado la literatura científica sin rodeos y descaradamente. Es un escándalo. El acceso abierto a la literatura científica, algo tan elemental y sin embargo quimérico a la fecha, es simplemente un aspecto del marco más amplio de las prácticas de Ciencia Abierta [4]. La Ciencia Abierta es ampliamente reconocida como un estándar superior del quehacer científico, que paulatinamente comienza a tomar un camino claro de implementación. Un avance prometedor en este sentido es la recomendación de la UNESCO sobre ciencia abierta. Este documento esencial define a la Ciencia como una construcción inclusiva: multilingüe, abierta, accesible, transparente, reutilizable, compartible, colaborativa y orientada al beneficio de la sociedad [5].Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin

A Divergent Strain of Culex pipiens-Associated Tunisia Virus in the Malaria Vector Anopheles epiroticus

Here, we report the draft genome sequence of a divergent strain ofCulex pipiens-associated Tunisia virus (CpATV) identified in the malaria vectorAnoph-eles epiroticus(CpATV-AnE). CpATV-AnE expands the reference virus sequence, intro-ducing an extended replicase with novel virga-like domains. Our results suggest thatthe host range of CpATV includesAnophelessp. mosquitoes.Instituto de Patología VegetalFil: Debat, Humberto J. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal (IPAVE). Córdoba; ArgentinaFil: Ribero, Jose M C. National Institute of Allergy and Infectious Diseases (NIAID-NIH). Laboratory of Malaria and Vector Research.Section of Vector Biology; Estados Unido

Dataset of the first transcriptome assembly of the tree crop “yerba mate” (Ilex paraguariensis) and systematic characterization of protein coding genes

This contribution contains data associated to the research article entitled “Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly” (Debat et al., 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus. This dataset (Supplementary files 1 and 2) consolidates the transcriptome-wide assembled sequences of I. paraguariensis with further comprehensive annotation of the protein coding genes of yerba mate via the integration of Arabidopsis thaliana databases. The generated data is pivotal for the characterization of agronomical relevant genes in the tree crop yerba mate -a non-model species- and related taxa in Ilex. The raw sequencing data dissected here is available at DDBJ/ENA/GenBank (NCBI Resource Coordinators, 2016) [2] Sequence Read Archive (SRA) under the accession SRP043293 and the assembled sequences have been deposited at the Transcriptome Shotgun Assembly Sequence Database (TSA) under the accession GFHV00000000.Fil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentin

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.Fil: Bejerman, Nicolas. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Dietzgen, Ralf G.. University of Queensland; Australi

An Integrated Physical Map of the Cultivated Hot Chili Pepper, Capsicum baccatum var. Pendulum

Capsicum baccatum var. Pendulum is the most frequently cultivated chili pepper in South America. This taxon is an outstanding source for breeding programs and genetic improvement in the genus, since its traits can be introgressed into C. annuum and related species to generate viable hybrids. In this study, the chromosome complement of C. baccatum var. Pendulum 2n = 24 was deeply characterized through a sequential combination of conventional and molecular cytogenetics approaches comprising Ag-NOR staining, heterochromatic fluorescence C-DAPI and CMA/DA/DAPI bandings and fluorescent in situ hybridization (FISH) of Capsicum-derived 5S and 18S-25S ribosomal genes and spacers probes. The attained markers were systematically integrated into a physical map which allows the identification of each individual chromosome. This is the first integrated physical map of C. baccatum var. Pendulum, which in conjunction with reported genetic linkage maps of Capsicum, would be useful for future high-density genetic mapping and whole-genome studies in C. baccatum and related taxa, as well as in breeding and genetic improvement programs in chili peppersInstituto de Patología VegetalFil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Universidad Nacional de Misiones. Instituto de Biotecnología de Misiones; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Universidad Nacional de Misiones. Instituto de Biotecnología de Misiones; Argentin

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomyInstituto de Patología VegetalFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; AustraliaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin