Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

Amisse, J. J. G.; Ndunguru, Joseph; Tairo, Fred; Ateka, Elijah; Boykin, Laura M.; Kehoe, Monica A.; Cossa, Nurbibi; Rey, Chrissie; Sseruwagi, Peter

doi:10.1111/ppa.13001

Cited by 11 publications

(11 citation statements)

References 40 publications

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“…Unfortunately, cassava production in sub‐Saharan Africa is currently limited by two viral diseases: cassava mosaic disease and cassava brown streak disease (CBSD), which have severe impacts on food and economic security across the entire region (Patil et al , ; Tomlinson et al , ). CBSD is caused by at least two viral species: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), collectively termed U/CBSVs (Mbanzibwa et al , 2011; Monger et al , ,b; Winter et al , ; Amisse et al , ). In cassava, U/CBSVs cause foliar chlorosis and root necrosis, and can cause yield losses of up to 100% in susceptible varieties (Kaweesi et al , ).…”

Section: Introductionmentioning

confidence: 99%

Cassava brown streak virus Ham1 protein hydrolyses mutagenic nucleotides and is a necrosis determinant

Tomlinson

Pablo‐Rodriguez

Bunawan

et al. 2019

Molecular Plant Pathology

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Summary Cassava brown streak disease (CBSD) is a leading cause of cassava losses in East and Central Africa, and is currently having a severe impact on food security. The disease is caused by two viruses within the Potyviridae family: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), which both encode atypical Ham1 proteins with highly conserved inosine triphosphate (ITP) pyrophosphohydrolase (ITPase) domains. ITPase proteins are widely encoded by plant, animal, and archaea. They selectively hydrolyse mutagenic nucleotide triphosphates to prevent their incorporation into nucleic acid and thereby function to reduce mutation rates. It has previously been hypothesized that U/CBSVs encode Ham1 proteins with ITPase activity to reduce viral mutation rates during infection. In this study, we investigate the potential roles of U/CBSV Ham1 proteins. We show that both CBSV and UCBSV Ham1 proteins have ITPase activities through in vitro enzyme assays. Deep‐sequencing experiments found no evidence of the U/CBSV Ham1 proteins providing mutagenic protection during infections of Nicotiana hosts. Manipulations of the CBSV_Tanza infectious clone were performed, including a Ham1 deletion, ITPase point mutations, and UCBSV Ham1 chimera. Unlike severely necrotic wild‐type CBSV_Tanza infections, infections of Nicotiana benthamiana with the manipulated CBSV infectious clones do not develop necrosis, indicating that that the CBSV Ham1 is a necrosis determinant. We propose that the presence of U/CBSV Ham1 proteins with highly conserved ITPase motifs indicates that they serve highly selectable functions during infections of cassava and may represent a euphorbia host adaptation that could be targeted in antiviral strategies.

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Section: Introductionmentioning

confidence: 99%

Cassava brown streak virus Ham1 protein hydrolyses mutagenic nucleotides and is a necrosis determinant

Tomlinson

Pablo‐Rodriguez

Bunawan

et al. 2019

Molecular Plant Pathology

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“…Field samples collection were performed differently for each batch of samples and the methods have been described in previous studies for Tanzanian (Ndunguru et al 2015), Kenyan (Ateka et al 2017) and Mozambican (Amisse et al 2019) samples. RNA extraction was performed from approximately 100mg of cassava leaf as described by the CTAB (cetyltrimethyl ammonium bromide) protocol (Lodhi et al 1994).…”

Section: Methodsmentioning

confidence: 99%

Peer Review #1 of "Genetic diversity and SNP’s from the chloroplast coding regions of virus-infected cassava (v0.2)"

2020

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Cassava is a staple food crop in sub-Saharan Africa, it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease (CMD) and Cassava brown streak disease (CBSD). Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Noninfected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya, and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the SNPs for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.

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“…In addition to the COVID-19 sample, we also analyzed a cassava sample from Mozambique that was con rmed to be infected with a cassava brown streak virus [20] (Supplemental Table 5). We ran ParaKraken with the original NCBI database and the JGI databases on the sample and con rmed the presence of the virus of interest.…”

Section: Assessment Of Virus Uniqueness and Abundancementioning

confidence: 99%

“…A cassava root RNA-Seq sample with a con rmed brown streak virus was obtained from Amisse et al [20] and ran through ParaKraken [17] to classify taxa. A BALsample with a con rmed COVID-19 infection was obtained from Wu et al [19].…”

Section: Cassava Coronavirus and Updated Viral Genomes Datasetsmentioning

confidence: 99%

“…To illustrate the broad use of our viral classi cation method, we applied our ParaKraken databases to a plant dataset containing rhizosphere, endosphere, and soil samples of two different Populus genotypes and a dataset of post mortem brain samples from individuals with Autism Spectrum Disorder (ASD) and controls [18]. We also utilize NCBI's viral sequences as a positive control to identify how unique viral sequences are to the individual isolate and to identify known viruses under infection conditions, such as COVID-19 infection in a bronchoalveolar lavage (BAL) sample [19] and cassava brown streak virus in a cassava sample [20].…”

Section: Introductionmentioning

confidence: 99%

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A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes

Garcia¹,

Simha²,

Garvin³

et al. 2020

Preprint

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BackgroundViruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples.MethodsTo identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken (a parallelized version of Kraken), a metagenomic/transcriptomic classifier. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2.ResultsTo illustrate the breadth of our utility for classifying viruses with ParaKraken, especially samples without virus-induced pathophysiology, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain tissue. In the Populus study, we identified genotype and compartment-specific viral signatures, while in the Autism study we identified a significant increase in abundance of eight viral sequences in post mortem brains. We also show the potential accuracy for classifying viruses by utilizing the NCBI viral databases to identify the uniqueness of viral sequences and to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples.ConclusionViruses represent an essential component of the microbiome. The ability to classify viruses represents the compulsory first step in better understanding their role in the microbiome. The viral classification method presented here allows for a more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members and can be used with any tool that utilizes a taxonomy for classification (such as Kraken).

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Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

Cited by 11 publications

References 40 publications

Cassava brown streak virus Ham1 protein hydrolyses mutagenic nucleotides and is a necrosis determinant

Cassava brown streak virus Ham1 protein hydrolyses mutagenic nucleotides and is a necrosis determinant

Peer Review #1 of "Genetic diversity and SNP’s from the chloroplast coding regions of virus-infected cassava (v0.2)"

A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes

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