Unraveling the genome and gene expression of Hibiscus chlorotic ringspot virus isolated from Hibiscus rosa-sinensis in Southwest Iran

Abstract

Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae) is one of the pathogens causing disease on Hibiscus rosa-sinensis (Chinese rose), an ornamental plant grown throughout the tropic and subtropic regions of the world. In a survey on Chinese hibiscus plants showing chlorotic ring spots leaves in Khuzestan Province, Southwestern Iran, HCRSV was identified and the complete genome of the first Iranian isolate of the virus, HCRSV-IR, was determined using Illumina RNA-Seq. The genome of HCRSV-IR was 3911 nucleotides long and potentially encodes seven open reading frames (ORFs) similar to previously known HCRSV isolates. Iranian isolate of virus showed the highest nucleotide sequence identity, 94.39 %, to the Brazil isolate (MK279671.1) Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae) is one of the pathogens causing disease on Hibiscus rosa-sinensis (Chinese rose), an ornamental plant grown throughout the tropic and subtropic regions of the world. In a survey on Chinese hibiscus plants showing chlorotic ring spots leaves in Khuzestan Province, Southwestern Iran, HCRSV was identified and the complete genome of the first Iranian isolate of virus, HCRSV-IR, was determined using Illumina RNA-Seq. The genome of HCRSV-IR was 3911 nucleotides long and potentially encodes seven open reading frames (ORFs) similar to previously known HCRSV isolates. Iranian isolate of the virus showed the highest nucleotide sequence identity, 94.39 %, to Brazil isolate (MK279671.1) Chinese hibiscus plants exhibiting chlorotic ringspot symptoms were surveyed in southwestern Iran to determine the presence of Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae). The complete sequence of the Iranian isolate of the virus, HCRSV-IR, was obtained using Illumina RNA-Seq, marking the first time this sequence has been documented. HCRSV-IR (Accession No. OP779319) has a genome comprising 3911 nucleotides, which encodes seven potential open reading frames (ORFs). Comparative analysis revealed that HCRSV-IR shares the highest nucleotide sequence identity (94.39 %) with an isolate from Brazil (MK279671.1). Analysis of the gene expression profile of the HCRSV-IR population infecting hibiscus plants indicated increased expression of the coat protein gene. Additionally, seventeen single nucleotide polymorphisms (SNPs) were identified within the viral variant populations from the infected hibiscus plants. These SNPs were located in coding regions across the entire genome, implying potential evolutionary significance. To the best of our knowledge, this study represents the first investigation into the molecular characterization of the complete genome of HCRSV, specifically infecting Chinese hibiscus in Iran.