Analysis of endophytic microbiome dataset from roots of black pepper (Piper nigrum L.) cultivated in the Central Highlands region, Vietnam using 16S rRNA gene metagenomic next-generation sequencing

Tran, Dinh Minh; Nguyen, Thi Huyen; Huynh, To Uyen; Do, Tu Oanh; Nguyen, Quang‐Vinh; Nguyen, Anh Dzung

doi:10.1016/j.dib.2022.108108

Cited by 12 publications

(14 citation statements)

References 5 publications

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“…Library preparation and 16S rRNA metagenomic sequencing were conducted as Tran et al. [6] , [7] , [8] described. Briefly, the V1–V9 regions of the 16S rRNA genes were amplified, and the Swift amplicon 16S plus internal transcribed spacer panel kit (Swift Biosciences, USA) was used to prepare libraries of 16S rRNA gene amplicons.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…Taxonomic and functional profiles of endophytic prokaryotes in the root sample were analyzed using the method described by Tran et al. [6] , [7] , [8] . Briefly, bcl2fastq was used to demultiplex raw basecall files.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…As Tran et al. described previously, the V1–V9 regions of the 16S rRNA genes were amplified [6] , [7] , [8] . Libraries of 16S rRNA gene amplicons were prepared using the Swift amplicon 16S plus ITS panel kit (Swift Biosciences, USA).…”

Section: Specifications Tablementioning

confidence: 99%

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Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data

Tran

2022

Data in Brief

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Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

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Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data

Tran

2022

Data in Brief

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“…Agronomically, the scope of mNGS technologies is expanding day by day. Researchers think microbial diversity data is essential for sustainable black pepper production [14]. The organisms that make up the plant microbiota provide the necessary nutrients for the growth and development of the plant.…”

Section: Figure 1 Applications Of Mngs Technology In Different Fieldsmentioning

confidence: 99%

“…Moreover, using metagenomic data to detect and control biotic stress factors affecting crop yield offers optimistic promises for the future. For example, the metagenomic method with 16 S rRNA barcodes was applied to samples obtained from black pepper roots grown in Vietnam [14].…”

Section: Figure 1 Applications Of Mngs Technology In Different Fieldsmentioning

confidence: 99%

Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnosing Plant Fungal Pathogens

Gökdemir¹,

İşeri²,

Sharma³

et al. 2022

Preprint

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Crop output is directly impacted by plant infections (with fungi as the major pathogen), making accurate diagnosis of these threats crucial. Developing technology and multidisciplinary approaches are turning to genomic analyses in addition to traditional culture methods in diagnosing fungal plant diseases. The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping identification of organisms, identification at the species level, illumination of metabolic pathways, and determination of microbiota. Moreover, the data obtained so far show that this new approach shows promise as an emerging new trend in fungal disease detection. Another approach covered by mNGS technologies, known as metabarcoding, enables use of specific markers specific to a genetic region and allows for genotypic identification by facilitating the sequencing of certain regions. Although the core concept of mNGS remains constant across applications, the specific sequencing methods and bioinformatics tools used to analyze the data do differ. In this review, we focus on how mNGS technology, including metabarcoding, is applied in fungal pathogenesis and its promising developments for the future.

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Root endophytic microbiome dataset of sugarcane (Saccharum officinarum L.) cultivated in the Central Highlands, Vietnam, established by the 16S rRNA metagenomics

Nguyen

Tran

2023

Data in Brief

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Analysis of endophytic microbiome dataset from roots of black pepper (Piper nigrum L.) cultivated in the Central Highlands region, Vietnam using 16S rRNA gene metagenomic next-generation sequencing

Cited by 12 publications

References 5 publications

Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data

Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data

Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnosing Plant Fungal Pathogens

Root endophytic microbiome dataset of sugarcane (Saccharum officinarum L.) cultivated in the Central Highlands, Vietnam, established by the 16S rRNA metagenomics

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