High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Ibaba, Jacques Davy; Gubba, Augustine

doi:10.3390/plants9101376

Cited by 17 publications

(12 citation statements)

References 139 publications

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“…The potential of nematodes for such work in Uganda led to initial work on PCR-based analysis of 18S rRNA gene sequences ( Nakacwa et al, 2013 ). Next generation sequencing supersedes that approach and has been applied to Plasmodium falciparum in Uganda ( Boyce et al, 2018 ) and the genomes of plant viruses in Africa including Uganda ( Ibaba and Gubba, 2020 ). Implementation of the approach for soil quality in Uganda is likely to be incremental.…”

Section: Discussionmentioning

confidence: 99%

Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored

Bell

Namaganda

Urwin

et al. 2021

Applied Soil Ecology

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Uganda faces a considerable challenge to match its food production to an annual population growth rate of 3%. Cooking bananas are the country's most produced staple crop but the annual national harvest is not increasing. The crop grows on infertile soils that are normally fertilised organically and often susceptible to erosion. Soil nematodes are well-established as bioindicators of soil quality that can support environmental monitoring and assessment of the sustainability of agricultural systems. These invertebrates are a highly ranked indicator of biodiversity with molecular approaches available. Consequently, we have applied next-generation DNA sequencing of soil nematodes to evaluate soil quality of Ugandan banana plantations. The aim is to establish a method for constructing an aspect of an environmental biosafety dossier with the future aim of assessing the impact of transgenic crops and improving current cropping systems. The soil samples did not differ significantly in any of the measured soil chemistry factors, soil texture or percentage of organic matter. Thirty taxons of soil nematodes other than the plant parasites were recovered from soil supporting nine banana plantations plus three each from coffee and banana-coffee interplants from East and West Uganda. Cluster analysis correctly allocated each plantation to the crop/intercrop being grown when based on the abundance of taxa rather than taxa presence or absence. This indicates that the host has considerable effects on the abundance of specific nematode species within the soil. Overall, nematodes were more abundant in soil from coffee plantations than from banana-coffee interplants with the lowest values being from fields supporting just banana. Only the basal and trophic diversity indices and the percentage of nematodes that are rapid colonisers varied between the three plantation types. The soil of all fifteen plantations can be classified as having a mature soil web condition with low physical disturbance, limited chemical stressors, moderately high nutrient enrichment and balanced decomposition channels.

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Section: Discussionmentioning

confidence: 99%

Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored

Bell

Namaganda

Urwin

et al. 2021

Applied Soil Ecology

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Section: Verbena Officinalis L Silene Latifolia Poir Rorippa × Prostrata Robinia Pseudoaccacia Lmentioning

confidence: 99%

“…Since 2010, studies using HTS to identify plant viruses have been conducted in 20 African countries, reviewed by Ibaba et al [35]. At least 29 host plants, including various economically important crops, ornamentals, and medicinal plants representing 18 different families have been used in HTS for virus detection and diagnostics [32,35]. The studies resulted in the detection of previously known and novel viruses from almost any host, confirming the wide distribution of plant viruses in different ecosystems and suggesting the importance of knowledge on the diversity, prevalence, and spatial distribution of viruses.…”

Section: Verbena Officinalis L Silene Latifolia Poir Rorippa × Prostrata Robinia Pseudoaccacia Lmentioning

confidence: 99%

Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities

Hasiów‐Jaroszewska

Boezen

Zwart

2021

Viruses

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High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection—often in the absence of disease symptoms—and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.

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“…Several comprehensive publications have reviewed the viruses affecting specific legume crops or production areas (i.e., [ 2 , 3 , 4 , 5 , 6 , 7 ]). However, the number of legume viruses identified continues to increase in the light of ongoing research, while in the era of metagenomics analysis, the application of new molecular technologies and high-throughput sequencing (HTS) technologies contribute highly to the discovery of new viruses [ 8 , 9 ]. Some of these novel viruses are officially classified, while others are still missing some critical features for their final taxonomic assignment.…”

Section: Introductionmentioning

confidence: 99%

An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics

Chatzivassiliou

2021

Plants

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Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized.

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High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Cited by 17 publications

References 139 publications

Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored

Next-generation sequencing of the soil nematode community enables the sustainability of banana plantations to be monitored

Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities

An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics

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