Benzoxazinoids influence rhizosphere establishment and root colonization by PGPB

Опубликована: Март 26, 2024

Benzoxazinoids influence rhizosphere establishment and root colonization by PGPBBenzoxazinoids (BXs) form a group of secondary metabolites produced many plants the grass family (Poaceae).Release activation BXs upon pathogen attack strongly suppresses disease pest species foraging herbivorous insects in areal parts plant.At same time, are constitutively set free predominantly during early plant development, where they affect microbial interaction.Hydroxamic acid BX derivatives such as 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA), 2,4dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) 2-hydroxy-4,7-dimethoxy-1,4benzoxazin-3-one (HDMBOA) general more reactive but have shorter half-life than lactam 2-benzoxazolinone (BOA) 6-methoxy-2-benzoxazolinone (MBOA).Regardless, MBOA is efficient at suppressing several fungal pathogens influences rhizospheric interactions over generations plants.Key to understanding plant-microbe symbiosis knowledge about means chemical communication between symbionts, physiological changes those signaling molecules evoke on each symbiont.Therefore, we aimed study mechanisms which an interspecies exchange information precedes initiation establishment.In order gain insight into these processes, investigated how mediate growth promoting bacteria (PGPB) Azospirillum brasilense Ab-V5, Bacillus thuringiensis RZ2MS9, Pantoea agglomerans 33.1 Pseudomonas protegens Pf-5, adverse effect pathogenic Fusarium.We found that bacterial response exogenic was specific for PGPB dose dependent.Curiously, Fusarium strains isolated from non-BX-producing hosts were susceptible low doses, while maize (from BX-producing host) tolerant.Root patterns Ab-V5 Pf-5 studied detail, showing preference crevices hairs primary sites.MBOA did not biofilm formation Arabidopsis roots improved.Finally, results vitro experiments cross validated transcriptomic assays chemotaxis regulatory protein showed relative upregulation 0.05 mM treatment could correlated amount differential expressed genes related production with concentration.The transcriptome however, little affected, consistent previously obtained results.We conclude intermediate concentrations stimulates motile high evokes metabolic switch preparation colonization.

Язык: Английский

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A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 27, 2024

Abstract Genomic resources for macroalgae are increasingly important conservation and commercial management, however the generation of such continues to be hampered by difficulties in isolation suitable DNA. Even when DNA has been isolated that otherwise appears high quality, samples may not perform well during sequencing process. We here compare Oxford Nanopore long-read results three species those non-macroalgal find macroalgal tend lead rapid decline number available pores resulting reduced yield. LC-MS analysis would considered reveals derived from dried is enriched polyphenol-DNA adducts – which inhibition. Our findings have wide-ranging implications genomic macroalgae, example long read herbarium specimens, suggest a need use fresh tissue wherever possible genome sequencing.

Язык: Английский

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High-molecular-weight DNA extraction for broadleaved and conifer tree species

Silvae genetica/Silvae Genetica, Год журнала: 2024, Номер 73(1), С. 85 - 98

Опубликована: Янв. 1, 2024

Abstract Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step these projects is the successful extraction of high-molecular-weight DNA high quality and sufficient quantity, which imperative for long-read sequencing. The trees limited difficult conduct. To achieve extraction, modification protocol necessary. Here, we present a from broadleaved Fraxinus excelsior conifer Taxus baccata . nuclei isolation divided into two main steps, i.e. separation buffer using Nanobind® plant kit by Pacific Biosciences (PacBio). can be different obtain quality, used Oxford Nanopore Technologies (ONT) PacBio ONT four preparations excel-sior resulted read length N50 values (12.91-38.19 kb) total base output (5.81-23.17 Gb), emphasizing complex nature pipeline DNA. HiFi produced circular consensus with an average 12.9 kb 13.59 kb. Altogether, this study presents challenging discusses several important points that considered when adapting additional species.

Язык: Английский

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Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef

Foods, Год журнала: 2024, Номер 13(20), С. 3304 - 3304

Опубликована: Окт. 18, 2024

Six hundred million cases of disease and roughly 420,000 deaths occur globally each year due to foodborne pathogens. Current methods screen identify pathogens in swine, poultry, cattle products include immuno-based techniques (e.g., immunoassay integrated biosensors), molecular DNA hybridization PCR assays), traditional culturing. These are often used tandem screen, quantify, characterize samples, prolonging real-time comprehensive analysis. Next-generation sequencing (NGS) is a relatively new technology that combines DNA-sequencing chemistry bioinformatics generate analyze large amounts short- or long-read sequences whole genomes. The goal this project was evaluate the quantitative capabilities NGS Oxford Nanopore Technologies’ MinION sequencer through shotgun-based approach. This investigation explored correlation between known analyte (lambda as pathogenic bacterial surrogate) with data output, both presence absence background matrix (Bos taurus DNA). A positive linear observed concentration amount produced, number bases sequenced, reads generated matrix. In bovine DNA, sequenced were successfully mapped NCBI lambda reference genome. Furthermore, workflow from pre-extracted target identification took less than 3 h, demonstrating potential food safety rapid method for screening, identification, quantification.

Язык: Английский

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A cry for kelp: Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae

Journal of Phycology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 22, 2024

Abstract Genomic resources have yielded unprecedented insights into ecological and evolutionary processes, not to mention their importance in economic conservation management of specific organisms. However, the field macroalgal genomics is hampered by difficulties isolation suitable DNA. Even when DNA that appears high quality standard metrics has been isolated, such samples may perform well during sequencing process. We here compared Oxford Nanopore long‐read results for three species macroalgae those nonmacroalgal determined using samples, activity declined rapidly, resulting reduced yield. Chemical analysis would be considered revealed derived from dried was enriched polyphenol–DNA adducts (DNA with large polyphenols chemically attached it), which led inhibition. Of note, we observed strongest evidence inhibition sequence output silica gel—suggesting storage approaches appropriate destined sequencing. Our findings wide‐ranging implications generation genomic suggest a need develop new methods are more amenable or use fresh flash‐frozen tissue wherever possible genome

Язык: Английский

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Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Ноя. 12, 2024

The advent of Oxford Nanopore Technologies has undergone significant improvements in terms sequencing costs, accuracy, and read lengths, making it a cost-effective, readily accessible approach for analyzing microbial genomes. A major challenge bacterial whole genome by technology is the requirement higher quality quantity high molecular weight DNA compared to short-read platforms. In this study, using eight pathogenic bacteria, we evaluated quality, quantity, fragmented size distribution extracted obtained from three different commercial extraction kits, one automated robotic platform. Our results demonstrated variation yield purity among kits. ZymoBIOMICS Miniprep Kit (ZM) provided other kit-based extractions. All extractions were successfully performed on all twenty-four samples single MinION flow cell, with Nanobind CBB Big kit (NB) yielding longest raw reads. Fire Monkey HMW-DNA Extraction (FM) Roche MagNaPure 96 platform (RO) outperformed assembly, particularly gram-negative bacteria. Based our finding, recommend minimum coverage N50, appropriate each species, optimize assembly plasmid recovery. This will assist end-users selecting most effective method whole-genome only long-read nanopore sequences.

Язык: Английский

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A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 14, 2024

Abstract Background Oxford Nanopore Technologies’ MinION sequencer is a compact, USB-powered device that has been available since 2014. Since the release of earliest model, throughput and error rate platform have improved dramatically it become possible to consider sequencing assembly eukaryotic organisms using single nanopore flow cell. Here, we present sequence data, methylation analysis for Columbia (Col-0) accession model plant Arabidopsis thaliana . Further, demonstrate effect recent developments (specifically Q20+ chemistry basecaller improvements) had on read accuracy quality. Findings DNA extracted from leaves A. Col-0 was sequenced two cells, together amounting 115x coverage 135 Mb genome. Reads were assembled polished several bioinformatics pipelines data. We performed CpG directly this correlated well with previously published bisulfite dataset. Conclusions Our results suggest cell can generate sufficient data assemble genome 135Mb, indicate functional elements, unlock genomics researchers novel species $600 in under 5 days. Here full sets both nanopore-only assemblies. The presented here expected be particular interest those community, designing projects (with annotations), expanding our understanding epigenetics across tree life, university or high school practicals teaching epigenomics. Highlight evaluate software improvements ability complete conduct

Язык: Английский

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Comparison of direct RNA sequencing of Orthoavulavirus javaense using two different chemistries on the MinION platform

Journal of Virological Methods, Год журнала: 2024, Номер unknown, С. 115103 - 115103

Опубликована: Дек. 1, 2024

Rapidly identifying and sequencing viral pathogens in poultry flocks can substantially reduce economic loss especially during disease outbreaks. Current next generation technologies require multi-step laboratory-intensive workflows to generate sequence data which precludes field adaptation. In this study, we hypothesized that direct RNA (DRS) using an Oxford Nanopore Technology (ONT) MinION device would enable of the full-length genome Orthoavulavirus javaense (OAVJ), causative Newcastle disease, a major challenge. The demonstrate custom OAVJ-specific adapter paired with ONT DRS kits enables capture OAVJ RNAs. Further, new SQK-RNA004 chemistry flow cells, associated super accurate base calling workflow improves on read quality length compared previous SQK-RNA002 chemistry. This is first report method near member Paramyxoviridae family. While additional improvements are needed before widespread adaptation for rapid sequencing, has potential further studies into epitranscriptome its role infection pathogenesis.

Язык: Английский

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A CRISPR-based strategy for targeted sequencing in biodiversity science

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 30, 2023

Abstract Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples a diagnostic reference library. Widely used methods for barcoding and metabarcoding PCR amplicon sequencing identify taxa based on target sequences, but target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages some applications. We identified 54,837 guide RNAs that be useful enriching chloroplast across phylogenetically diverse plant species. then tested subset 17 vitro enrich sequence strands ranging size barcodes 1,428 bp entire genomes 121,284 bp. an Oxford Nanopore sequencer evaluate success both samples, which yielded mean on-target lengths 5,755-11,367 bp, depending experiment. Single-species experiments more reads greater accuracy, superior coverage. Comparing CRISPR-based strategies widely protocol with trn L-P6 marker, we obtained 66-fold increase length markedly better estimates relative abundance commercially prepared mixture Future work would benefit developing silico analyses especially when appropriate contig assembly cannot known priori . Prior developed protocols long-read our pioneered its use chromosome assemblies have over workflows short-read sequencing.

Язык: Английский

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