High‐throughput sequencing‐based detection and characterization of sugarcane viruses in Ethiopia

Author:

Abide Mereme1ORCID,Kidanemariam Dawit2,Kebede Misrak1,Knierim Dennis3,Margaria Paolo3,Menzel Wulf3ORCID,Abraham Adane14

Affiliation:

1. Department of Biotechnology Addis Ababa Science and Technology University Addis Ababa Ethiopia

2. Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa

3. Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures GmbH Braunschweig Germany

4. Department of Biological Sciences and Biotechnology Botswana International University of Science and Technology Palapye Botswana

Abstract

AbstractA virus discovery investigation using high‐throughput sequencing in sugarcane samples from Ethiopia revealed the presence of sugarcane mild mosaic virus (SCMMV, genus Ampelovirus) and sugarcane umbra‐like virus (SULV, genus Umbravirus). The genome sequences of two isolates of SCMMV and one SULV were determined. The sequences of the two SCMMV isolates were 13,005 nucleotides in length and showed ~73.5% nucleotide identity along the genome and ~90.2, 96.8, and 90.4% amino acid sequence identity among each other in the RdRp, CP, and HSP70h, respectively. Isolate SCMMV ET2 showed a close relationship to group A isolates from Colombia, the USA, and the Philippines, with amino acid sequence identity of the predicted virus proteins in the range of 94–98.9%. Conversely, SCMMV ET1 shared a closer relationship with group B isolates from Colombia, Ivory Coast, and Argentina, exhibiting a 93–99% amino acid sequence identity. The complete genome sequence of SULV, comprising 3041 nucleotides, exhibited the highest identity with its counterpart from South Africa (MN868593). These findings contribute to expanding our understanding of the viral diversity within the sugarcane crop in Ethiopia.

Publisher

Wiley

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