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      Assessment of Yam mild mosaic virus coat protein gene sequence diversity reveals the prevalence of cosmopolitan and African group of isolates in Ghana and Nigeria

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          Highlights

          • •

            Sequence diversity show lack of geographical association between isolates from Ghana and Nigeria.

          • •

            YMMV isolates from Ghana and Nigeria fall within four of the 11 monophyletic groups.

          • •

            Need for stringent control of germplasm exchange as infection is mainly by infected tubers.

          Abstract

          This study analyzed the genetic diversity of 18 Yam mild mosaic virus (YMMV, genus Potyvirus) isolates collected from field surveys in Ghana (N = 8) and Nigeria (N = 10) in 2012−13. The full coat protein (CP) encoding region of the virus genome was sequenced and used for comparison and phylogenetic analysis of the YMMV isolates available in the NCBI nucleotide database. The mean nucleotide (nt) diversity was 13.4% among the 18 isolates (17 from D. alata and one from D. rotundata), 11.4% within the isolates of Ghana and 7.4% within the isolates of Nigeria. The phylogenetic clustering of the 18 YMMV isolates did not show correlation with the country of origin, and they aligned with the reference sequences of four of the 11 YMMV monophyletic groups representing the cosmopolitan group and the African group of YMMV isolates. High sequence homology of 99% between the YMMV sequence from Nigeria (CP12-DaN6-1) and a previously reported sequence from Togo (GenBank Accession Number AF548514) suggests a prevalence of seed-borne virus spread within the region. Understanding YMMV sequence diversity in West Africa aid in the improvement of diagnostic assays necessary for virus indexing and seed certification.

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          Multiple sequence alignment with the Clustal series of programs.

          R Chenna (2003)
          The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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            Molecular criteria for genus and species discrimination within the family Potyviridae.

            J Antoniw, C Fauquet, J. Adams (2005)
            A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.
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              Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus.

              Rory Hillocks, N. Maruthi, P Wasswa … (2010)
              Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV. 2009 Elsevier B.V. All rights reserved.
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                Author and article information

                Contributors
                Chukwuemeka K. Nkere
                Journal
                Journal ID (nlm-ta): Curr Plant Biol
                Journal ID (iso-abbrev): Curr Plant Biol
                Title: Current Plant Biology
                Publisher: Elsevier B.V
                ISSN (Electronic): 2214-6628
                Publication date PMC-release: 1 September 2020
                Publication date (Electronic): September 2020
                Volume: 23
                Electronic Location Identifier: 100156
                Affiliations
                [a ]International Institute of Tropical Agriculture, PMB, 5320, Ibadan, Nigeria
                [b ]Department of Crop Protection and Environmental Biology, University of Ibadan, Nigeria
                [c ]National Root Crops Research Institute, Umudike, PMB, 7006, Umuahia, Nigeria
                [d ]CSIR-Crops Research Institute, Kumasi, P.O. Box 3785, Fumesua, Ghana
                [e ]Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, ME4 4TB, UK
                Author notes
                [* ]Corresponding author: National Root Crops Research Institute (NRCRI) Umudike, PMB 7006, Umuahia, Nigeria. nkerechukwuemeka@ 123456yahoo.com
                Article
                Publisher ID: S2214-6628(20)30037-2 Publisher ID: 100156
                DOI: 10.1016/j.cpb.2020.100156
                PMC ID: 7444016
                SO-VID: a65a3319-70c5-4dd6-a680-36321feeb7d9
                Copyright © © 2020 The Author(s)
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 3 January 2020
                Date revision received : 21 April 2020
                Date accepted : 1 May 2020
                Categories
                Subject: Article

                Keywords: ymmv, yam mild mosaic virus,ymv, yam mosaic virus,yam,dioscorea spp.,virus,ghana,nigeria
                Data availability:
                Keywords: ymmv, yam mild mosaic virus, ymv, yam mosaic virus, yam, dioscorea spp., virus, ghana, nigeria

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