Molecular diversity of cotton leaf curl Gezira virus isolates and their satellite DNAs associated with okra leaf curl disease in Burkina Faso

Abstract

Okra leaf curl disease (OLCD) is a major constraint on okra (Abelmoschus esculentus) production and is widespread in Africa. Using a large number of samples representative of the major growing regions in Burkina Faso (BF), we show that the disease is associated with a monopartite begomovirus and satellite DNA complexes. Twenty-three complete genomic sequences of Cotton leaf curl Gezira virus (CLCuGV) isolates associated with OLCD, sharing 95 to 99% nucleotide identity, were cloned and sequenced. Six betasatellite and four alphasatellite (DNA-1) molecules were also characterized. The six isolates of betasatellite associated with CLCuGV isolates correspond to Cotton leaf curl Gezira betasatellite (CLCuGB) (88 to 98% nucleotide identity). One isolate of alphasatellite is a variant of Cotton leaf curl Gezira alphasatellite (CLCuGA) (89% nucleotide identity), whereas the three others isolates appear to correspond to a new species of alphasatellite (CLCuGA most similar sequence present 52 to 60% nucleotide identity), provisionally named Okra leaf curl Burkina Faso alphasatellite (OLCBFA). Recombination analysis of the viruses demonstrated the interspecies recombinant origin of all CLCuGV isolates, with parents being close to Hollyhock leaf crumple virus (AY036009) and Tomato leaf curl Diana virus (AM701765). Combined with the presence of satellites DNA, these results highlight the complexity of begomoviruses associated with OLCD.

Figure 1

Maximum likelihood tree based on the complete DNA-A sequences of twenty-three Cotton leaf curl Gezira virus isolates from Burkina Faso (in bold; see Table 2 for isolates name and acronyms), plus additional sequences from African and Asian monopartite and bipartite begomoviruses. Begomovirus acronyms used are Cotton leaf curl Gezira virus (CLCuGV), Hollyhock leaf crumple virus (HoLCrV), Cotton leaf curl Bangalore virus (CLCuBV), Okra yellow vein mosaic virus (OYVMV), Tomato leaf curl Togo virus (ToLCTGV), Tomato leaf curl Ghana virus (ToLCGHV), Tomato leaf curl Nigeria virus (ToLCNGV), South African cassava mosaic virus (SACMV), Tomato yellow leaf curl Sardinia virus (TYLCSV), Tomato leaf curl Sudan virus (ToLCSDV), Tomato yellow leaf curl Mali virus (TYLCMLV), Tomato yellow leaf curl virus-Mild (TYLCV-Mld), Pepper yellow vein Mali virus (PepYVMV), Tomato curly stunt virus (ToCSV), Tobacco leaf curl Zimbabwe virus (TbLCZV), Tomato leaf curl Mali virus (ToLCMV), Okra yellow crinkle virus (OYCrV) and Malvastrum leaf curl virus (MaLCV). For the complete description of isolate descriptors refer to Fauquet et al. (2008). Four genetic groups (G1 to G4) have been defined on the presence or absence of recombination events (Figure 4), and are represented here.

Figure 2

Maximum likelihood tree based upon alignments of selected sequences of betasatellite genomes. The betasatellite acronyms used are as described by Briddon et al. [40]: Cotton leaf curl Gezira betasatellite (CLCuGB), Papaya leaf curl betasatellite (PaLCuB), Ageratum yellow vein Sri Lanka betasatellite (AYVSLB), Sida yellow mosaic China betasatellite (SiYMCNB), Malvastrum yellow vein betasatellite (MaYVB), Cotton leaf curl Multan betasatellite (CLCuMB) and Cotton leaf curl alphasatellite (CLCuA-[PK:1:99]) (Outgroup).

Figure 3

Maximum likelihood tree based on selected alphasatellite sequences. Acronyms used are as described by Mubin et al. [17]: Malvastrum yellow mosaic alphasatellite (MaYMA), Sida leaf curl alphasatellite (SiLCuA), Gossypium darwinii symptomless alphasatellite (GDSA), Okra leaf curl alphasatellite (OLCA), Cotton leaf curl Rajastan alphasatellite (CLCuRA), Tomato yellow leaf curl China alphasatellite (TYLCCNA), Tobacco curly shoot alphasatellite (TbCSA), Sida yellow vein Vietnam alphasatellite (SiYVVNA), Okra leaf curl alphasatellite (OLCA), Okra leaf curl Cameroon alphasatellite (OLCCMA) and Cotton leaf curl Gezira betasatellite (CLCuGB) (outgroup).

Figure 4

Recombinant regions (a, b and c) detected within the African isolates of CLCuGV sequences using RDP3. Four genetic groups (G1 to G4) have been defined on the presence or absence of recombination events. The genome at the top of the figure corresponds to the schematic representation of sequences below. Region coordinates are nucleotide positions of detected recombination breakpoints in the multiple sequence alignment used to detect recombination. Wherever possible, parental sequences are identified. "Major" and "Minor" parents are sequences that were used, along with the indicated recombinant sequence, to identify recombination. Whereas for each identified event the minor parent is apparently the contributor of the sequence within the indicated region, the major parent is the apparent contributor of the rest of the sequence. Note that the identified "parental sequences" are not the actual parents but are simply those sequences most similar to the actual parents in the analysed dataset. Recombinant regions and parental viruses were identified using the RDP (R), GENECONV (G), BOOTSCAN (B), MAXIMUM CHI SQUARE (M), CHIMAERA (C), SISTER SCAN (S) and 3Seq (T) methods. Whereas upper case letters imply a method detected recombination with a multiple comparison corrected P-value < 0.01, lower case letters imply the method detected recombination with a multiple comparison corrected P-value <0.05 but > = 0.01.