Association of papaya leaf curl virus and DNA satellite molecules with leaf curl disease of sunhemp (Crotalaria juncea L.) in India

Crotalaria juncea L., known as brown hemp, Indian hemp, Madras hemp, or sunhemp, is a tropical Asian plant of the legume family, Fabaceae and considered to have originated in India. Sunhemp is a multipurpose tropical and subtropical legume grown for green manure and is having good potential of biological nitrogen fixation, drought tolerance and as fodder for cattle. Despite these benefits, the crop is an alternative host for many begomoviruses. Samples from sunhemp plants exhibiting leaf curl disease symptoms were collected from Varanasi and Mirzapur districts of Uttar Pradesh State, India. To know the status of the begomovirus in ten sunhemp samples, the total genomic DNA was isolated and PCR assay for detection of begomoviruses using degenerate primers specific to the DNA-A component of the begomoviruses. This resulted in the expected amplicon of 1.2 kb representing the partial genome of begomoviruses and indicated that ten samples collected from sunhemp plants showing leaf curl are associated with begomovirus. Sequencing and analysis of amplified partial (1.2 kb) genome revealed the sequence identity of more than 95% between them among them. Therefore, one representative sunhemp sample was selected for amplifying complete genome of the virus (DNA-A/DNA-A homologue) using rolling circle amplification and their associated DNA satellites by PCR using specific primer pairs. Amplified products were cloned and sequenced. Pairwise comparison of the complete viral genome (DNA-A) infecting sunhemp using SDT (Sequence Demarcation tool) showed its maximum nucleotide (nt) identity of 92.7% with papaya leaf curl virus. Further, sequence analysis of beta and alphasatellite showed their maximum nt identity of 93.7 to 95.2% with radish leaf curl betasatellite and 96.5% with cotton leaf curl Multan alphasatellite, respectively. Recombination analysis of complete viral genome and DNA satellites indicates that the DNA-A component of the begomovirus and alphasatellite isolated from sunhemp might have originated from recombination of already existing begomoviruses and alphasatellites. However, there is no evidence of recombination found in betasatellite associated with leaf curl disease of sunhemp. This is the first report of papaya leaf curl virus, radish leaf curl betasatellite and cotton leaf curl Multan alphasatellite associated with leaf curl disease of sunhemp from India.

Automated summary

Crotalaria juncea L., known as sunhemp, is a tropical legume plant with good potential for nitrogen fixation and drought tolerance. However, it can act as an alternative host for begomoviruses, with sequencing analysis showing a high sequence identity between the virus and associated DNA satellites.