In silico identification of sugarcane (Saccharum officinarum L.) genome encoded microRNAs targeting sugarcane bacilliform virus.

Xiaowen Hu,Xiaoyan Feng,Muhammad Aleem Ashraf,Shuzhen Zhang,Muhammad Shahzad Iqbal,Linbo Shen,Fakiha Ashraf,Shunmugiah Veluchamy Ramesh

doi:10.1371/journal.pone.0261807

Abstract

Sugarcane bacilliform virus (SCBV) is considered one of the most economically damaging pathogens for sugarcane production worldwide. Three open reading frames (ORFs) are characterized in the circular, ds-DNA genome of the SCBV; these encode for a hypothetical protein (ORF1), a DNA binding protein (ORF2), and a polyprotein (ORF3). A comprehensive evaluation of sugarcane (Saccharum officinarum L.) miRNAs for the silencing of the SCBV genome using in silico algorithms were carried out in the present study using mature sugarcane miRNAs. miRNAs of sugarcane are retrieved from the miRBase database and assessed in terms of hybridization with the SCBV genome. A total of 14 potential candidate miRNAs from sugarcane were screened out by all used algorithms used for the silencing of SCBV. The consensus of three algorithms predicted the hybridization site of sof-miR159e at common locus 5534. miRNA-mRNA interactions were estimated by computing the free-energy of the miRNA-mRNA duplex using the RNAcofold algorithm. A regulatory network of predicted candidate miRNAs of sugarcane with SCBV-ORFs, generated using Circos-is used to identify novel targets. The predicted data provide useful information for the development of SCBV-resistant sugarcane plants.

Highlights

Sugarcane bacilliform viruses (SCBVs) are classified into the Badnavirus genus of the Caulimoviridae family
ORF1 is composed of 557 nucleotides (618–1175 nt), encoding a hypothetical protein (P1) with 185 amino acids,while ORF2 is composed of 370 nucleotides (1176–1546 nt) codes for a virion-associated DNA binding protein (P2) with 123 aa
The current study demonstrates that SCBV genome components (ORF1, ORF2, and ORF3) are susceptible to targeting by a set of consensual sugarcane miRNAs

Summary

Introduction

Sugarcane bacilliform viruses (SCBVs) are classified into the Badnavirus genus of the Caulimoviridae family. These viruses are composed of monopartite, circular, non-enveloped bacilliforms that are (30 × 120–150 nm) in size, with a double-stranded DNA (ds-DNA)- genome of approximately 7.2–9.2 Kbp in size [1]. The genome of SCBV constitutes three major open reading frames (ORFs) that are located on the ‘plus DNA strand’ with a single discontinuity [2].

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Conclusion