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Metagenomic-based screening and molecular characterization of yams-infecting viruses by High-Throughput Sequencing and Pox marker | SciTechnol

Journal of Marine Biology & Oceanography.ISSN: 2324-8661

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Special Issue Article, Maria Biology And Oceanography Vol: 0 Issue: 0

Metagenomic-based screening and molecular characterization of yams-infecting viruses by High-Throughput Sequencing and Pox marker

Abstract

To date  Dioscorea (Yams) in Kenya is a neglected crop, notwithstanding its potential as food and in pharmaceutics as a drug source. Research on neglected crops specifically Dioscorea is a sure way of sensitizing the scientific community and policy makers about it. Several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. 
High-throughput Sequencing (HTS) and use of POX marker methods are progressively being used in the discovery of new plant viral genomes and metabolism processes in plants.
In this study, i will employ HTS on yam to determine whether any undiscovered viruses will be present that would restrict the international distribution of yam germplasm. The finding will work on discovery of a new virus sequence present. Thirty one (31) yam samples will be tested and have tentatively named as virus “yam virus Y” (YVY) .The metabolic reaction which may bring mutation will be tested by use of Peroxidase marker as they achieve the Arabiodisis process in metabolic of the organism. Complete genome sequences of two YVY viral isolates will be assembled and further finding will be done to text five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein as yam  contain dioscorin which is full of protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further finding work will be needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.

Keywords: RNA-Seq; virus detection; Betaflexiviridae; next-generation sequencing; HTS

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