Biology subjects

Fernandez, F. D.

Publications and source records attributed to Fernandez, F. D..

8 recordsLinked to original sources

bioRxiv2025

Endophytic bacteria Bacillus velezensis NKG50 as a potential biocontrol agent of Ascochyta blight on chickpea

One of chickpea crops most devastating and economically relevant fungal diseases is Ascochyta rabiei, the causal agent of Ascochyta blight. The traditional agricultural management of the disease requires a complex combination of cultural, chemical, and genetic strategies. To develop a more effective management strategy, with low economic and environmental costs, we isolated 43 endophytic bacteria from asymptomatic chickpea plants native to our soils region. We tested their antifungal effect with mycelial growth and conidia germination inhibition tests. Our best candidate was NKG50 isolate, which inhibited A. rabiei growth by more than 85% in the dual test, more than 65% by cell-free supernatants, and inhibited conidia germination by 90%. This antagonistic ability was confirmed in leaflet and greenhouse assays, with a significant reduction in disease severity in both scales. The isolated NKG50 genome was completely sequenced and identified as Bacillus velezensis NKG50. We found 13 gene clusters associated with secondary metabolites, and five of them with an unknown function and or nature previously reported for B. velezensis. This study demonstrated for the first time that B. velezensis NKG50 is a strong candidate for the biocontrol of Ascochyta blight in Argentina.

microbiology↗

bioRxiv2025

First genomic resource of Candidatus Phytoplasma pyri associated to pear decline

This study reports the draft genome of Candidatus Phytoplasma pyri strain P1, isolated from Argentina, marking the first global sequencing of this species. The genome assembly consisted of 16 contigs, with a total length of 575,431 bp, a GC content of 20.35%, and 125X coverage. A total of 536 genes were annotated, including those related to metabolism, genetic information processing, and signaling. Phylogenetic analysis placed Candidatus Phytoplasma pyri within the 16SrX group, supporting its classification as a distinct species from Candidatus Phytoplasma mali and Candidatus Phytoplasma prunorum, despite their close evolutionary proximity. The investigation also identified 17 secreted proteins, including homologs of known effectors such as SAP39 and SAP41, as well as conserved proteins associated with virulence mechanisms. A homologue of the Imp immunodominant membrane protein was also characterized, revealing conserved gene organization across related strains. These findings contribute to the understanding of Candidatus Phytoplasma pyri pathogenic and provide valuable genomic data for future research. This study highlights the importance of expanding phytoplasma genomics, as it provides a crucial first step in understanding Candidatus Phytoplasma pyri and its role in plant pathology

genomics↗

bioRxiv2024

First Draft Genome of the Corn Leafhopper Dalbulus maidis: A Transparent, Open, and Updateable Resource in the Context of Agricultural Emergence

The corn leafhopper, Dalbulus maidis, is a significant pest affecting maize crops, causing extensive economic losses and posing a threat to food security. This study presents the first draft genome of D. maidis as part of a comprehensive initiative to generate critical information for effective pest management and long-term control strategies. The genome sequencing is being conducted using a hybrid approach that integrates Oxford Nanopore Technologies (ONT) and Illumina platforms, ensuring high accuracy and depth. The initial genome assembly comprises approximately 580 Mb, with an N50 of 50,453 bp, indicating a draft assembly quality. The genomes completeness, evaluated using BUSCO, stands at 68.6%, underscoring the thoroughness of the assembly. This first draft genome is designed to be a "living genome," subject to continuous updates as new sequencing data become available. By providing an open and updatable genomic resource, this study aims to facilitate ongoing research and foster collaborative efforts in developing innovative solutions to mitigate the impact of D. maidis on maize cultivation.

genomics↗

bioRxiv2024

Analysis arbuscular mycorrhizal fungi (AMF) community composition associated with alkaline saline sodic soils

Marginal soils affected by salinity, sodicity and alkalinity decrease crop productivity. In this context, a viable alternative strategy lies in the remediation of degraded lands using beneficial microorganisms. This study aims to characterize native arbuscular mycorrhizal fungal (AMF) communities by sequencing PCR amplicons that cover most of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region, and a portion of the large subunit (LSU) rRNA, employing Oxford Nanopore Technologies (ONT). Three field sites, with varying crop conditions, were selected: a patch with no crop growth (Site 1), a patch with corn stubble (Site 2), and a patch with wheat plants exhibiting 15 days of growth (Site 3). Soil analyses revealed distinct characteristics - alkaline saline sodic soil (ASS) for Site 1, moderately alkaline soil (A) for Site 2, and neutral soil (N) for Site 3. ONT sequencing yielded a total of 4,040,470 raw reads from which 19.13% survived after quality and length filter. Reads were grouped in 556 clusters, of which 222 remained after bioinformatic analysis. Despite moderate error rates in 9.4.1, flowcells chemistry, using a clustering and polishing approach facilitated the ecological analysis and allowed a better taxonomic resolution. Bioinformatic analysis showed no significant differences in AMF diversity among soils. However, results suggest the dominance of Glomeraceae and Acaulosporaceae families, specifically the genera Glomus and Acaulospora in ASS soil. Further exploration is required to better understand their role in promoting plant growth under adverse conditions. The study highlights the significance of cutting-edge sequencing tools in advancing the comprehension of essential symbiotic relationships for sustainable agriculture in challenging environments.

plant biology↗

bioRxiv2021

Genome characterization of 'Candidatus Phytoplasma meliae' (isolate ChTYXIII)

Candidatus Phytoplasma meliae (subgroups 16SrXIII-G and XIII-C) has been reported in association to chinaberry yellowing disease in Argentina, Bolivia and Paraguay. In Argentina, this disease constitutes a major phytosanitary problem for chinaberry forestry production. To date, no genome information of this phytoplasma and others from 16SrXIII-group has been published, hindered its characterization at genomic level. Here we analyze the draft genome of Candidatus Phytoplasma meliae strain ChTYXIII obtained from a chinaberry-infected plant using a metagenomics approach. The draft assembly consists of twenty-one contigs with a total length of 751.949 bp. The annotation contains 669 CDSs, 34tRNA and one set of rRNA operons. Metabolic pathways analysis indicated that the ChTYXIII contains the complete core genes for glycolysis and functional sec system for translocation of proteins. The phylogenetic relationships inferred 132 single copy genes (orthologues core) analysis revealed that Ca. P. meliae constitutes a clade closely related to the Ca. australiense and Ca. P. solani. Thirty-one putative effectors were identified, among which a homologue to SAP11 was found and others that have only been described in this pathogen. This work provides relevant genomic information for Ca. P. meliae and constitutes the first genome described for the group 16SrXIII (MPV).

genomics↗

bioRxiv2020

Diversity analysis of amp gene sequences in the 'Candidatus Phytoplasma meliae'

Phytoplasmas are plant pathogenic bacteria transmitted by insects. As endosymbiotic bacteria that lack a cell wall, their membrane proteins are in direct contact with host cytoplasm. In phytoplasmas the immunodominant membrane proteins (IDPs), are the most abundant proteins of the cell membrane. The antigenic membrane protein (Amp), one of the three types of IDPs, is characterized by a positive selection pressure acting in their extracellular domain. In South America, the Candidatus Phytoplasma meliae has been associated to chinaberry yellows disease. In the present work, we describe for the first time the structure, phylogeny and selection pressure of amp gene in sixteen Candidatus Phytoplasma meliae isolates. Our results indicate that amp gene sequences preserve the structure, large extracellular domain flanked by to hydrophobic domains in the N- (signal peptide) and C-termini (transmembrane), previously described in its orthologues and high divergence in the amino acids residues from extracellular domain. Moreover, a positive selection pressure was detected predominantly in this region confirming previous reports.

microbiology↗

bioRxiv2019

'Candidatus Phytoplasma platensis', a novel taxon associated with daisy (Bellis perennis) virescence and related diseases in South America

Bellis perennis virescence (BellVir) phytoplasma affects ornamental daisies in Argentina. It has been previously classified within the X-disease group, subgroup III-J, which is one of the most important and widely distributed in South America, affecting diverse plant hosts. In this study, we compared 16S rRNA, ribosomal proteins rpIV and rps3, secA and immunodominant proteins imp and idpA genes of BellVir phytoplasma with previously described Candidatus Phytoplasma species. The 16S rRNA gene of strain BellVir shared less than 97.5% with all previously described Ca. Phytoplasma taxa except for Ca. Phytoplasma pruni. According to the recommended rules for the description of novel taxa within Ca. Phytoplasma, it should be considered as Ca. P. pruni-related strain. However, multilocus analysis showed further molecular diversity that distinguished BellVir phytoplasma from Ca. Phytoplasma pruni. Besides, BellVir phytoplasma and 16SrIII-J related strains have a geographical distribution restricted to South America, where Ca. P.pruni has not been detected. Two insect vectors have been reported to transmit 16SrIII-J phytoplasmas, which have not been found to transmit Ca. Phytoplasma pruni. Having a wide host range, they have not been detected in Prunus persica. Therefore, based on multilocus sequence analyses, specific vector transmission and geographical distribution, we propose the recognition of the novel phytoplasma species Ca. Phytoplasma platensis, within the X-disease clade, with Bellis perennis virescence phytoplasma as the reference strain.

molecular biology↗

bioRxiv2018

Molecular characterization of effector protein SAP54 in Bellis Virescence Phytoplasma (16SrIII-J)

Phytoplasmas are wall-less bacteria, with a parasitic life style responsible for numerous plant diseases worldwide. The genomic landscape of phytoplasmas has been scarcely studied. Nevertheless, since the introduction of next generation sequencing technologies, genome wide studies of these pathogens are flourishing and a handful of phytoplasmas genomes are available in public databases. In South America, phytoplasmas from 16SrIII group (X-disease) are the most widely distributed, and only a draft genome from a phytoplasmas 16SrIII-J infected periwinkle from Chile has been generated (Phytoplasma Vc33). Here, in grafting experiments we characterized the phenotypic signatures of an Argentinian daisy derived isolate of a 16SrIII-J phytoplasma (Bellis Virescence Phytoplasma) infecting periwinkle. Moreover, we applied a pipeline for genome wide annotation of the Vc33 genome and identified the effector protein SAP54. We then employed the obtained data to amplify, clone, sequence and characterize a SAP54 orthologue protein of Bellis Virescence Phytoplasma. Structural and phylogenetic analyses suggested that the identified SAP54 is highly conserved, and that its co-divergence among phytoplasma is not directly consistent with the evolutionary trajectories derived from rRNA analyses. The results gathered here could provide the basis for reverse genetics experiments using 16SrIII-J SAP54 proteins to assess their eventual influence in pathogenesis.

molecular biology↗