Molecular identification and characterization of two rubber dandelion amalgaviruses

The Amalgaviridae family is composed of persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. A single Amalgavirus genus has been assigned to this family, presenting only four recognized species, corresponding to plant infecting viruses with dsRNA monopartite genomes of ca. 3.4 kb. Here, we present the genomic identification and characterization of two novel viruses detected in rubber dandelion (Taraxacum kok-saghyz). The sequenced isolates presented genomes of 3,409 and 3,413 nt long, including two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Phylogenetic insights based on the detected virus sequences suggest them to be members of two new species within the Amalgavirus genus. Multiple independent RNAseq data suggest that the identified viruses have a dynamic distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant hosts. We propose the names rubber dandelion latent virus 1 & 2 to the detected amalgaviruses; the first viruses to be associated to this emergent and sustainable natural rubber crop.Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Zinan Luo. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Iaffaldano, Brian J. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Xiaofeng Zhuang. Ohio State University. Department of Horticulture and Crop Science; Estados UnidosFil: Cornish, Katrina. Ohio State University. Department of Horticulture and Crop Science; Estados Unido

A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis.

Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on - 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. The possible derivation of this virus from a fungus associated with C. quitensis is discussed

An insight into the sialotranscriptome and virome of Amazonian anophelines

Background: Saliva of mosquitoes contains anti-platelet, anti-clotting, vasodilatory, anti-complement and anti-inflammatory substances that help the blood feeding process. The salivary polypeptides are at a fast pace of evolution possibly due to their relative lack of structural constraint and possibly also by positive selection on their genes leading to evasion of host immune pressure. Results: In this study, we used deep mRNA sequence to uncover for the first time the sialomes of four Amazonian anophelines species (Anopheles braziliensis, A. marajorara, A. nuneztovari and A. triannulatus) and extend the knowledge of the A. darlingi sialome. Two libraries were generated from A. darlingi mosquitoes, sampled from two localities separated ~ 1100 km apart. A total of 60,016 sequences were submitted to GenBank, which will help discovery of novel pharmacologically active polypeptides and the design of specific immunological markers of mosquito exposure. Additionally, in these analyses we identified and characterized novel phasmaviruses and anpheviruses associated to the sialomes of A. triannulatus, A. marajorara and A. darlingi species. Conclusions: Besides their pharmacological properties, which may be exploited for the development of new drugs (e.g. anti-thrombotics), salivary proteins of blood feeding arthropods may be turned into tools to prevent and/or better control vector borne diseases; for example, through the development of vaccines or biomarkers to evaluate human exposure to vector bites. The sialotranscriptome study reported here provided novel data on four New World anopheline species and allowed to extend our knowledge on the salivary repertoire of A. darlingi. Additionally, we discovered novel viruses following analysis of the transcriptomes, a procedure that should become standard within future RNAseq studies. © 2019 The Author(s)

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology (2021) 166:3567–3579. https://doi.org/10.1007/s00705-021-05266-wIn March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This work was also supported in part with federal funds from the National Cancer Institute (NCI), National Institutes of Health (NIH), under Contract No. 75N91019D00024, Task Order No. 75N91019F00130 to I.C., who was supported by the Clinical Monitoring Research Program Directorate, Frederick National Lab for Cancer Research. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of The National Biodefense Analysis and Countermeasures Center, a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges partial support from the Special Research Initiative of Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Part of this work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001030), the UK Medical Research Council (FC001030), and the Wellcome Trust (FC001030).S

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

55 Pág.In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infec tious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowl edges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1021494. The funders had no role in the design of the study; in the collection, analysis, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Department of the Army, the U.S. Department of Defence, the U.S. Department of Health and Human Services, including the Centres for Disease Control and Prevention, the U.S. Department of Homeland Security (DHS) Science and Technology Directorate (S and T), or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The U.S. departments do not endorse any products or commercial services mentioned in this publication. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S.Government retains a non-exclusive, paid up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes.Peer reviewe

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV

On the value of preprints: an early career researcher perspective

Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent, public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision and resubmission causing redundant peer review. This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. ECRs face changes in the academic landscape including the increased interdisciplinarity of life sciences research, expansion of the researcher population and consequent shifts in employer and funding demands. The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal managed peer-review, can play a key role in addressing these ECR challenges. Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback and facilitating collaborations. While there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted. The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting needs to be addressed. We provide a perspective from an interdisciplinary group of early career researchers on the value of preprints and advocate the wide adoption of preprints to advance knowledge and facilitate career development.</jats:p

CARACTERIZACION MORFOLOGICA Y CROMOSOMICA DE COMMELINA BENGHALENSIS L. (COMMELINACEAE) DE ARGENTINA

Commelina benghalensis is a small herb native to tropical Africa and Asia but introduced elsewhere. In America it wasfound growing at open fields, border of woods and cultivated areas (south USA, Mexico, West Indies, French Guiana,Brazil, Bolivia, Paraguay) as a weed or invasive plant and its difficult manage causes economic damages in diverseagroecosystems all over the world. Commelina benghalensis was found at a border of Misiones´ forest (Argentina,Misiones Province, Guaraní Departament, El Soberbio, 27º17’54.5’’S; 54º12’19’’W) and classical cytogenetic techniqueswere applied in order to analyze its genetic system. Commelina benghalensis is a diploid with 2n = 2x = 22 median sizechromosomes (4.05 - 6.60 µm) and 55.04 µm/genome. Its karyotype, 8m + 10sm + 4st is unimodal (A2 = 0.14 / R = 1.63)and slightly asymmetrical (A1 = 0.44 / i = 34.75 / r&gt;2 = 0.55) (3A Stebbins category). Chromosome pair No. 11 (st) hasa terminal macrosatellite in the short arm and presumably carry the active NOR. Microsporogenesis is normal andproduces viable polen grains (&gt;80%). Meiotic behaviour is regular. In PMC at diakinecis / metaphase I, 11 bivalents wereobserved, mainly rings (92.7%) with distal chiasmata (96.7%) and an average of chiasmata / bivalent = 1.90. The meioticsystem in conjuntion with a particular breeding system promotes a high genetic homogeneity, and suggests that thisspecies has coadapted features with adaptative advantages allowing an invader behaviour.Commelina benghalensis es una hierba pequeña, nativa de Africa y Asia tropical, aunque en la actualidad crece en casitodo el mundo. En América se la reporta creciendo en campo abierto, borde de bosques y áreas cultivadas (sur de USA,México, Antillas, Guyana Francesa, Brasil, Bolivia, Paraguay) como maleza o invasora y su difícil control causa pérdidaseconómicas importantes en diversos agroecosistemas de todo el mundo. Commelina benghalensis fue encontrada en unborde de selva misionera (Argentina, Provincia de Misiones, Departamento Guaraní, El Soberbio, 27º17’54,5’’S;54º12’19’’W), y se aplicaron técnicas citogenéticas tradicionales para analizar su sistema genético. Commelina benghalensises diploide con 2n = 2x = 22 cromosomas de tamaño medio (4,05 - 6,60 µm) y 55,04 µm/genoma. Su cariotipo, 8m + 10sm+ 4st es unimodal (A2 = 0,14 / R = 1,63) y levemente asimétrico (A1 = 0,44 / i = 34,75 / r&gt;2 = 0,55) (Categoría 3A deStebbins). El par nº 11 (st) presenta un macrosatélite terminal y constricción secundaria en el brazo corto que posiblementelleve los NOR activos. La microsporogénesis es normal y produce polen viable (&gt;80%). El comportamiento meiótico esregular. En CMP en diacinesis / metafase I se observan 11 bivalentes, mayormente cerrados (92,7%) con quiasmasdistales (96,7%) y un promedio de quiasmas / bivalente = 1,90. Su sistema meiótico junto con un particular sistemareproductivo promueven una alta homogeneidad genética y sugieren caracteres coadaptados que le confieren a estaespecie ventajas adaptativas como colonizadora

FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae)

ABSTRACT We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus