Molecular characterization of Hollyhock leaf curl virus and associated DNA-satellites infecting Malva parviflora in Pakistan

Figures & data

Fig. 1 (Colour online) Malva parviflora plants exhibiting vein yellowing and chlorosis symptoms.

Table 1. Primer sequences used in this study.

Primers	Primer sequences	PCR product size
AC1048	GGRTTDGARGCATGHGTACATG	~579 kb
AV494	GCCYATRTAYAGRAAGCCMAG
SonchA_F	TGATCGACGGCCTGTGGAT	~2.8kb
SonchA_R	CGGACCAAGAAGAACATCA
Beta01	GGTACCACTACGCATCGCAGCAGCC	~1.4 kb*
Beta02	GGTACCTACCCTCCCAGGGGTACAC
SOB_F	TTCTATTGGGCCAATTTAATGG	~1.4 kb
SOB_R	GTCAGATCCAGTCAAGCCC
DNA101	CTGCAGATAATGATGTAGCTTACCAG	~1.4 kb
DNA102	CTGCAGATCCTCCACGTGTATAG

*A partial betasatellite sequence (~850 nt) was obtained during this study.

Table 2. Predicted open reading frames (ORFs) for the begomovirus and associated DNA-satellites identified from Malva parviflora.

ORFs	Position (nt coordinates)	Size of ORFs (nt)	Coding capacity (amino acids)	Predicted product size (KDa)
Pre-coat protein (V2)	132–479	347	115	13.3
Coat protein (CP)	292–1062	770	256	29.7
Replication associated protein (Rep)	2602–1511	1091	363	40.8
Transcriptional activator protein (TrAp)	1614–1162	452	150	17.0
Replication enhancer protein (REn)	1469–1065	404	134	15.7
C4	2445–2143	302	100	11.0
BetaC1 (βC1)	557–201	365	118	13.8
Rep-A	81–1028/87–1034*	947/947*	315/315*	36.8/36.7*

*Sonch31a2/Sonch31a3.

Fig. 2 Phylogenetic dendrograms based on complete nt sequences of (a) begomovirus, (b) betasatellite, and (c) alphasatellite isolates, using Neighbour-Joining (NJ) algorithm in MEGA7. All the isolates identified from Pakistan in this study are shown in bold white text on black background. Horizontal lines represent nt substitutions per site. Numeric values at branch nodes are representing per cent bootstrap values higher than 60 (1000 replicates). All isolates used for comparison are represented by their respective accession numbers in the trees. All abbreviations for begomovirus, alpha- and betasatellite isolates are according to Brown et al. (2012) and Briddon et al. (2012), respectively.

Brown JK, Fauquet CM, Briddon RW, Zerbini M, Moriones E, Navas-Castillo J. 2012. Geminiviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. London: Associated Press; 351–373.

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