First record of a novel begomovirus and satellites associated with leaf curl disease of passion fruit from India

Abstract

Passion fruit is an important fruit crop grown in parts of southern and north-eastern states of India. Leaf curl symptoms typical to begomovirus infection were observed on passion fruit plants at three locations of Madikeri District, Karnataka State, India. The disease incidence ranged from 10–20% in all the locations. In order to determine if the begomovirus was associated with leaf curl disease of passion fruit, 20 infected samples collected from different locations were subjected to PCR analysis using primers specific to begomovirus. This resulted in an expected PCR product of ~1.2 kb. Sequence analysis of these products revealed that they have more than 98% similarity among them and have similarity with other begomoviruses. Complete genome sequencing of begomovirus associated with one sample (PF1 collected from CHES, Madikeri) was done using RCA. Further, sequencing of betasatellite and alphasatellite was done after PCR amplification using specific primers. Complete DNA-A sequence of PF-isolate with other begomoviruses revealed that it shared nucleotide (nt) identity of 87.8 to 88.8% with Ageratum enation virus. This indicated the association of a novel begomovirus with leaf curl disease of passion fruit in India, for which we propose the name, Passion fruit leaf curl virus (PFLCuV) [IN-Kar-18]. PFLCuV associated betasatellite shared 98.3% sequence identity with Tomato leaf curl Bangladesh betasatellite, while alphasatellite had 95.7% sequence identity with Cotton leaf curl Multan alphasatellite. Recombinant analysis indicated a major component of PFLCuV DNA-A may have originated from a recombination of earlier reported begomoviruses. Recombination as well as GC plot analysis showed that the recombination occurred in the genome regions having low GC content regions of PFLCuV. However, there is no evidence of recombination in alphasatellite and betasatellite associated with leaf curl disease of passion fruit. This is the first record of a novel begomovirus and satellites associated with leaf curl disease of passion fruit from India.

Keywords

• begomovirus
• passion fruit
• phylogenetic analysis
• recombination
• sequence demarcation tool (sdt)