Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach

Abstract

Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

“…Up to now, most HTS studies have been focused on virus identification and characterization in cultivated plants ( Stobbe and Roossinck, 2014 ). In contrast, metagenomic studies on wild plants have been scarcer ( Stobbe and Roossinck, 2014 ), but have confirmed that virus infections are common in nature ( Muthukumar et al, 2009 ; Claverie et al, 2018 , 2019 ; Susi et al, 2019 ) and may not cause any recognizable symptoms in wild plants in natural settings. These studies further reveal an abundance of persistent viruses (i.e., viruses that do not move between cells in plants but are transmitted in a strictly vertical manner via gametes) ( Roossinck, 2010 ).…”

“…Other approaches like Markov profile ( Mistry et al, 2013 ) or k-mer analyses ( Wood et al, 2019 ) can be used to try to identify novel virus species but without totally solving this issue since their performances are either incomplete or not properly known. Moreover, read assignment can be refined using statistical phylogenetic placement methodology, as recently illustrated by a study focusing on the appropriate phylogenetic position of viral metagenomic reads on a reference phylogenetic Mastrevirus tree ( Claverie et al, 2019 ). Beside these homology-based annotation methods, sequence-independent strategies have been developed to identify novel viral sequences without using sequence databases, e.g., through the examination of characteristics of virus-derived small RNAs ( Aguiar et al, 2015 ).…”

Shotgun Metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants

“…Also, there is an increase in the abundance of animals and birds disease causing Circovirus (Gillespie et al 2009), plant disease causing Babuvirus, Begomovirus and Nanovirus (Lal et al 2020;Fiallo-Olivé and Navas-Castillo 2020), bacteria infecting Bdellomicrovirus, Spiromicrovirus and Inovirus (Hyman and Abedon 2012;Roux et al 2019) and human disease causing Norovirus (Robilotti et al 2015). At axis 2, there is a strong positive loadings for N4-like phages, monocotyledonous plants infecting Mastrevirus and algae infecting Chlorovirus (Van Etten et al 2020;Buttimer et al 2018;Claverie et al 2019). These viruses particularly the phages and other bacteria infecting viruses are responsible for controlling bacterial phytopathogens and ensuring adequate plants protection in the fertilized soils.…”

Post-COVID-19 Action: Guarding Africa’s Crops against Viral Epidemics Requires Research Capacity Building That Unifies a Trio of Transdisciplinary Interventions

“…In Africa, HTS has been used for the detection of viruses from crops such as common bean (Phaseolus vulgaris) [12][13][14][15][16], maize (Zea mays) [17][18][19], sweet potato (Ipomoea batatas) [20][21][22], papaya (Carica papaya) [23], pumpkin (Cucurbita pepo) [24,25], fluted pumpkin (Telfairia occidentalis) [26], cassava [27][28][29], yam (Dioscorea spp.) [30,31], cowpea (Vigna unguiculate) [32] and in Poaceae plants [33]. These forages into HTS have led to the detection of known viruses and the discovery of many novel virus species (Table 1).…”