TaxonKit: A practical and efficient NCBI taxonomy toolkit

Shen, Wei; Ren, Hong

doi:10.1016/j.jgg.2021.03.006

Cited by 201 publications

(130 citation statements)

References 24 publications

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“…NCBI taxonomy assignments were retrieved using the option lineage from the taxonkit tool available at https://github.com/shenwei356/taxonkit 39 . All NCBI RdRp sequences were grouped according to their placement within the realm Riboviria , kingdom Orthornavirae (which includes all the RdRp-encoding RNA viruses), using both order and phylum ranks according to the current ICTV virus classification (https://talk.ictvonline.org/taxonomy/).…”

Section: Methodsmentioning

confidence: 99%

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Charon

Buchmann

Sadiq

et al. 2022

Preprint

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Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the known diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motif, as well as pre-built RdRp alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some sequences cluster into potential new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position, which might provide new insights into the structure, function and evolution of viral RdRps.

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Section: Methodsmentioning

confidence: 99%

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Charon

Buchmann

Sadiq

et al. 2022

Preprint

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“…Throughout this study, taxonomic names of prokaryotes were managed using the NCBI taxonomy system ( 68 ) and TaxonKit v0.8.0 ( 69 ), and fasta and fastq files were formatted using SeqKit v0.16.1 ( 70 ). R 4.0.5 ( 71 ) was used for data visualization.…”

Section: Methodsmentioning

confidence: 99%

Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

Mise

Masuda

Senoo

et al. 2021

mSphere

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Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases.

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“…All viral sequences were firstly downloaded with the GenBank format from the NCBI GenBank database on September 14 th , 2020. Viruses that were isolated from plant samples were obtained with the help of Taxonkit [37]. Viruses that have plants registered as their hosts were defined as plant viruses.…”

Section: Integration Of Viruses From Public Databasesmentioning

confidence: 99%

Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts

et al. 2022

Preprint

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Plant viruses cause huge damage to commercial crops, yet the studies towards plant viruses are limited and the diversity of plant viruses are under-estimated yet. This study built an up-to-date atlas of plant viruses by computationally identifying viruses from the RNA-seq data in the One Thousand Plant Transcriptomes Initiative (1KP) and by integrating plant viruses from public databases, and further built the Plant Virus Database (PVD, freely available at http://47.90.94.155/PlantVirusBase/#/home) to store and organize these viruses. The PVD contained 3,206 virus species and 9,604 virus-plant host interactions which were more than twice that reported in previous plant virus databases. The plant viruses were observed to infect only a few plant hosts and vice versa. Analysis and comparison of the viromes in the Monocots and Eudicots, and those in the plants in tropical and temperate regions showed significant differences in the virome composition. Finally, several factors including the viral group (DNA and RNA viruses), enveloped or not, and the transmission mode of viruses, were found to have no or weak associations with the host range of plant viruses. Overall, the study not only provides a valuable resource for further studies of plant viruses, but also deepens our understanding towards the genetic diversity of plant viruses and the virus-host interactions.

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TaxonKit: A practical and efficient NCBI taxonomy toolkit

Cited by 201 publications

References 24 publications

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts

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