Detection and molecular characterization of a new begomovirus associated with mosaic disease of Malachra capitata (Malvaceae) Buddhadeb Roy 1 & Ang Rinzing Sherpa 1 Received: 4 May 2018 /Accepted: 14 August 2018 /Published online: 21 August 2018 # Australasian Plant Pathology Society Inc. 2018 Abstract During a survey from March 2013 to October 2015, in Barasat, West Bengal, India, symptoms suggestive of begomovirus infection were observed in Malachra capitata. The occurrence of begomovirus on M. capitata was confirmed by symptomatol- ogy, polymerase chain reaction (PCR), Southern blot analysis and nucleotide analysis of the whole genome sequence. Sequence analysis showed that the virus had 90.6% identity with available sequences of Tomato leaf curl New Delhi virus (ToLCNDV). We propose that the new begomovirus be named Malachra yellow mosaic virus (MalYMV). To the best of our knowledge, this is the first time the complete genome of the MalYMV, infecting M. capitata in West Bengal, India, has been sequenced. Keywords Begomovirus . Malachra capitata . PCR . Southern blot . Detection . Genome Begomoviruses (family Geminiviridae) are among the most eco- nomically important plant viruses. They are efficiently transmit- ted by the whitefly (Bemisia tabaci), resulting in crop losses estimated to exceed billions of U.S. dollars annually and threat- ening food security (Stansly and Naranjo 2010). Begomoviruses affect production of a wide range of important crops, including beans, cassava, cotton, squash, sweet potato, and tomato. Two of the most devastating diseases caused by begomoviruses are to- mato leaf curl disease, widely distributed around the world (Lefeuvre et al. 2010), and cassava mosaic disease, which has reached pandemic levels in African countries (Legg et al. 2014). Weed species act as reservoir hosts for many economically im- portant plant virus diseases. Weeds infected with begomoviruses have been reported from different geographic areas of the world and have been described as natural hosts of various begomoviruses (Hallan et al. 1998; Khan et al. 2012). Malachra capitata (Family Malvaceae) is a common and fre- quently occurring weed species in India. It is widely distributed in cultivated and uncultivated land, wasteland, railway tracks, and road sides. It has some economic importance, as it is grown as a fibre plant in India, and formerly also in Cuba. The leaves and flowers are recorded in the Venezuelan Pharmacopoea. In some regions, roots and leaves are used as remedies for the many dis- ease conditions such as pain, diarrhoea, convulsion, hepatic cir- rhosis, inflammation, pyrexia, ulcer, dementia, healing of wounds (Ames et al. 1981; Rice-Evans et al. 1997; Bhowal and Yawalikar 2015). It is also used for bathing purposes (Tiwari et al. 1998). During a survey in the summer seasons of 2013 and 2015, in Barasat, West Bengal, India, specimens of M. capitata exhibit- ed the typical symptoms of a begomovirus infection, including leaf curling, leaf mosaic, leaf yellowing and stunted growth (Fig. 1). Symptomatic leaves were collected from different fields at Barasat and total DNA was extracted from the using the CTAB method (Ghosh et al. 2009) with some modification. Extracts were tested for the presence of begomoviruses by PCR using an indigenously designed begomovirus specific degener- ate primer pair (Roy et al. 2015). Of 14 samples, 12 had pos- itive PCR reactions. This indicates a begomovirus infection in symptomatic plants with amplification of parts of the AV1, AC3 and AC2 genes fragment of approx. ~760 bp length (Fig. 2a). For the Southern blot analysis, we designed a biotin labelled probe (5’-ATRRTHTGGATGGAYGARAACAT -3′). The 5′ end of the probe was biotinylated and used for the detection of geminiviruses from the total sap of infected plant samples. Briefly, about 5 μl of freshly prepared sap was blotted on a nitrocellulose membrane and air dried. The membrane was then UV-cross linked for 30 min under UV-Cross Linker * Ang Rinzing Sherpa ang2001@gmail.com Buddhadeb Roy buddhabotany@gmail.com 1 Department of Botany, West Bengal State University, Malikapur, Berunanpukuria, 24 North Parganas, Barasat, Kolkata, West Bengal 700126, India Australasian Plant Disease Notes (2018) 13: 30 https://doi.org/10.1007/s13314-018-0315-4