Complete genome sequence of Mesorhizobium ciceri strain R30, a Rhizobium used as a commercial inoculant for Chickpea in Argentina

We report the complete genome sequence of Mesorhizobium ciceri strain R30, a rhizobium strain recommended and used as a commercial inoculant for chickpea in Argentina. The genome consists of almost 7 Mb, distributed into two circular replicons: a chromosome of 6.49 Mb and a plasmid of 0.46 Mb.This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PID2020-113207GBI00 funded by MCIN/AEI/10.13039/501100011033); by “ERDF: A Way of Making Europe” (P20_0047), funded by the Junta de Andalucía PAIDI/FEDER/EU; and by the Biotechnology and Biosciences Research Council (BBSRC). We are grateful to Plateforme de Microbiologie Mutualisée (P2M) and the Pasteur International Bioresources network (PIBnet) and to Institut Pasteur Paris for providing the resources for Illumina sequencing. We thank O.G.C. at the Wellcome Centre for Human Genetics for the sequencing data and B.M.R.C. for processing (supported by Wellcome Trust Core Award grant 203141/Z/16/Z and the NIHR Oxford BRC). We are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN-UMR3569 CNRS, Université de Paris, Centre National de Référence Virus des Infections Respiratoires (dont la grippe) and to F. Sgarlatta for proofreading the manuscript

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity.

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19

Propagation of seminal toxins through binary expression gene drives could suppress populations

Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this restriction may be relaxed by using a double gene drive design to spread a split binary expression system. One drive carries a dominant lethal/toxic effector alone and the other a transactivator factor, without which the effector will not act. Only after the drives reach sufficiently high frequencies would individuals have the chance to inherit both system components and the effector be expressed. We explore through mathematical modeling the potential of this design to spread dominant lethal/toxic alleles and suppress populations. We show that this system could be implemented to spread engineered seminal proteins designed to kill females, making it highly effective against polyandrous populations. © 2022, The Author(s).Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Complete genome sequence of Bradyrhizobium sp. strain C-145, a nitrogen-fixing Rhizobacterium used as a peanut inoculant in Argentina

We present the complete genome sequence of Bradyrhizobium sp. strain C-145, one of the most widely used nitrogen-fixing rhizobacteria for inoculating peanut crops in Argentina. The genome consists of 9.53 Mbp in a single circular chromosome and was determined using a hybrid long- and short-read assembly approach.This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), the Spanish Ministerio de Ciencia e Innovación (research grant PID2020-113207GB-I00), ERDF (European Regional Development Funds), and the Biotechnology and Biosciences Research Council (BBSRC). It was also supported by Wellcome Trust Core Award grant number 203141/Z/16/Z and the NIHR Oxford BRC. We thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the sequencing data. We are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN—UMR3569 CNRS, Université de Paris, Centre National de Référence Virus des Infections Respiratoires (dont la grippe); to Plateforme de Microbiologie Mutualisée (P2M) and the Pasteur International Bioresources network (PIBnet); to Institut Pasteur Paris for providing the resources for Illumina sequencing; and finally, to F. Sgarlatta for proofreading the manuscript

Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant Clinical Strain from Argentina Harboring blaNDM-1

We report here the draft genome sequence of a NDM-1-producing Acinetobacter bereziniae clinical strain, HPC229. This strain harbors both plasmid and chromosomal resistance determinants towards different β-lactams and aminoglycosides as well as several types of multidrug efflux pumps, most likely representing an adaptation strategy for survival under different environments.Fil: Brovedan, Marco. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Marchiaro, Patricia M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Morán-Barrio, Jorgelina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Revale, Santiago. Instituto de Agrobiotecnología Rosario (INDEAR); Argentina.Fil: Cameranesi, Marcela. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Brambilla, Luciano. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Viale, Alejandro M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina.Fil: Limansky, Adriana S. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET); Argentina

Deciphering the phylogenetic affiliation of rhizobial strains recommended as chickpea inoculants in Argentina

Chickpea (Cicer arietinum L.) is globally cultivated due to its high nutritional value. As with other legumes, its success depends greatly on its inoculation with effective symbiotic rhizobial strains. Since its agricultural importance as an alternative winter crop in Argentina is very recent, there are limited phylogenetic studies on the affiliation and origin of the two strains used for its inoculation here. We attempted to define their specific identity through a multilocus sequence approach on seven housekeeping genes (phylogeny and average nucleotide identity), as well as on the basis of 16S rRNA gene sequence and nodC gene analysis. The strains were accurately and conclusively corroborated as M. ciceri and M. mediterraneum species, and their denominations were found to be associated to originally described chickpea-nodulating strains

Soil and rhizosphere bacterial diversity in maize agro-ecosystem.

ABSTRACT.Management practices used in maize production have an impact on soil agro- ecosystems where different microbial communities coexist. Soil inhabiting bacteria are numerous and diverse, but we know very little about their ecological distribution. Here we analyzed the bacterial community diversity in the rhizosphere of two transgenic maize cultivars, in agricultural soil before sowing and in non-cultivated soil in an experimental site in the south region of Uruguay. We followed two culture-independent methods: DGGE (denaturing gradient gel electrophoresis) and 454-pyrosequencing of 16S rRNA gene amplicon. Through pyrosequencing, the three environments analyzed presented differences in terms of bacterial composition. However, no differences were found in the relative abundance of the ten most represented phyla in the rhizosphere of the two cultivars at different phenological stages. We found significant differences of Bacteroidetes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia phyla when comparing agricultural and non-cultivated soils, as well as a significant enrichment of members of the phylum Gemmatimonadetes in all rhizosphere samples compared to soil. Through DGGE analysis we evidenced that maize rhizosphere bacterial communities changed at different phenological stages in both cultivars. We also provided baseline information about bacterial specific taxa within maize agro- ecosystem for further evaluation of possible rhizosphere bacterial community shifts of genetically modified maize cultivars under different management practices.Copyright © Canadian Center of Science and Educatio

Deciphering the phylogenetic affiliation of rhizobial strains recommended as chickpea inoculants in Argentina

Chickpea (Cicer arietinum L.) is globally cultivated due to its high nutritional value. As with other legumes, its success depends greatly on its inoculation with effective symbiotic rhizobial strains. Since its agricultural importance as an alternative winter crop in Argentina is very recent, there are limited phylogenetic studies on the affiliation and origin of the two strains used for its inoculation here. We attempted to define their specific identity through a multilocus sequence approach on seven housekeeping genes (phylogeny and average nucleotide identity), as well as on the basis of 16S rRNA gene sequence and nodC gene analysis. The strains were accurately and conclusively corroborated as M. ciceri and M. mediterraneum species, and their denominations were found to be associated to originally described chickpea-nodulating strains

A reference floral transcriptome of sexual and apomictic Paspalum notatum.

Background Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. Results We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types. Raw data originated from floral samples collected from premeiosis to anthesis was assembled in three libraries: i) sexual (SEX), ii) apomictic (APO) and iii) global (SEX + APO). A group of physicallysupported Paspalum mRNA and EST sequences matched with high level of confidence to both sexual and apomictic libraries. A preliminary trial allowed discovery of the whole set of putative alleles/paralogs corresponding to 23 previously identified apomixis-associated candidate genes. Moreover, a list of 3,732 transcripts and several co-expression and protein –protein interaction networks associated with apomixis were identified. Conclusions The use of the 454/Roche FLX+ transcriptome database will allow the detailed characterization of floral alleles/paralogs of apomixis candidate genes identified in prior and future work. Moreover, it was used to reveal additional candidate genes differentially represented in apomictic and sexual flowers. Gene ontology (GO) analyses of this set of transcripts indicated that the main molecular pathways altered in the apomictic genotype correspond to specific biological processes, like biotic and abiotic stress responses, growth, development, cell death and senescence. This data collection will be of interest to the plant reproduction research community and, particularly, to Paspalum breeding projects.</p