Abstract
Iris yellow spot virus (IYSV) is an important pathogen of Allium species worldwide. It has a tripartite genome consisting of the large (L), medium (M) and small (S) RNA segments. Despite its worldwide distribution, very few complete gene and genome sequences are available in public databases. The aim of this study was to obtain full gene sequences of a garlic-infecting IYSV isolate by next-generation sequencing (NGS) for understanding its evolution. Total RNA was extracted from an IYSV-positive garlic leaf and sequenced on the Illumina HiSeq platform using paired-end chemistry 125 × 125 bp reads. The quality of raw reads was assessed using FastQC software before trimming with Trimmomatic version 0.36. The resultant paired-end sequences were used for both de novo and reference-based genome assembly. The resultant consensus gene sequences were analyzed using SIAS (for sequence identity and composition), ExPASy (for protein molecular weight) and ORF Finder (for open reading frame identification). Three full gene sequences, that is, nucleocapsid (N), nonstructural protein (NSs) and movement protein (NSm) were recovered. The N gene did not display any distinct clustering patterns based on geographical locations and was most identical to an onion-infecting isolate from Serbia (Accession KT272878). The NSs and NSm genes clustered closely with homologous sequences of IYSV isolates that were retrieved from GenBank and EMBL. This study lays the foundation for complete genome studies of IYSV in Zimbabwe. Key words: Allium species, emerging pathogen, reverse transcription polymerase chain reaction (RT-PCR), serology, tospovirus.
Highlights
Iris yellow spot virus, IYSV, is an important emerging pathogen of Allium species worldwide responsible for causing significant yield and quality losses in alliaceous and ornamental crops (Bag et al, 2015)
The non-structural movement (NSm) protein is responsible for virus particle movement during systemic infection, while the two glycoproteins serve as virus attachment proteins (Bandla et al, 1998)
The 236-bp bands were visualized from samples that were IYSV-positive after electrophoresis on 1.5% agarose gel stained with SYBR Safe Gel stain (Life Technologies, USA)
Summary
IYSV, is an important emerging pathogen of Allium species worldwide responsible for causing significant yield and quality losses in alliaceous and ornamental crops (Bag et al, 2015). It was first isolated and characterized in iris (Iris holandica) in The Netherlands (Cortês et al, 1998) and has been confirmed to be present in over 40 countries worldwide (CABI, 2018). The S RNA is ambisense and encodes the non-structural (NSs) protein in the viral sense strand and the nucleocapsid (N) protein in the antiviral sense strand. IYSV is currently known to be transmitted by two thrips species, Thrips tabaci and Frankliniella fusca in a persistent and propagative mode (Srinivasan et al, 2012)
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