Mobilisation into cotton and spread of a recombinant cotton leaf curl disease satellite

Summary. Analysis of a DNA β satellite associated with a recently identified cotton leaf curl disease (CLCuD) strain indicated it to be recombinant, with most of the molecule originating from CLCuD DNA β but with some sequence from a satellite isolated from tomato. Analysis of both archival (pre 2001) and recent cotton samples, shows the recombinant satellite is confined to a small area but was not present in cotton prior to 2001. This indicates that the recombinant DNA β was recently mobilized into cotton, likely from tomato, and that recombination plays a role in the evolution of these satellites.     

Transmission of cotton leaf curl disease: answer to a long-standing question

Cotton leaf curl disease (CLCuD) has been a major constraint to cotton production across Pakistan and northwestern India since the early 1990s. The disease is caused by a number of begomoviruses, including Cotton leaf curl Multan virus (CLCuMuV), which associate with a specific host range and symptom determining betasatellite known as Cotton leaf curl Multan betasatellite (CLCuMuB). Bemisia tabaci is a complex of cryptic species that consists of numerous (>?44) morphologically indistinguishable and, at least partially, reproductively isolated species. CLCuD has recently been introduced into parts of China but has not, at least so far, become a problem in the major cotton regions. The disease in China has been shown to be caused by CLCuMuV with CLCuMuB, which is believed to have been introduced from South Asia in ornamental plants. To understand the basis for this lack of spread of CLCuD into the cotton-growing areas of China, Pan et al. (Phytopathology 108:1172–1183, 2018) investigated the transmission of CLCuMuV/CLCuMuB by B. tabaci. The study showed that, of the four cryptic B. tabaci species investigated, only the cryptic species Asia II 1 was able to efficiently transmit CLCuMuV/CLCuMuB. Significantly, Asia II 1 is not present in the major cotton-growing regions of China. The results of Pan et al. (Phytopathology 108:1172–1183, 2018) are discussed with particular emphasis on the situation of CLCuD in Pakistan and northwestern India, which differs significantly from the situation in China.     

Molecular characterization of Chilli leaf curl virus and satellite molecules associated with leaf curl disease of Amaranthus spp

Amaranthus, collectively known as amaranth, is an annual or short-lived perennial plant used as leafy vegetables, cereals and for ornamental purposes in many countries including India. During 2011, leaf samples of Amaranthus plants displaying leaf curling, leaf distortion, leaf crinkling and yellow leaf margins were collected from Banswara district, Rajasthan in India. Full-length clones of a monopartite begomovirus, a betasatellite and an alphasatellite were characterized. The complete nucleotide sequence of the isolated begomovirus features as a typical ‘Old World’ begomovirus with the highest nucleotide per cent identity with Chilli leaf curl virus and hence, considered as an isolate of Chilli leaf curl virus. The complete nucleotide sequences of betasatellite and alphasatellite possess maximum nucleotide identity with Tomato yellow leaf curl Thailand betasatellite and Chilli leaf curl alphasatellite, respectively. This is the first report of the association of chilli-infecting begomovirus and satellite molecules infecting a new host, Amaranthus, causing leaf curl disease.     

Identification of dna components required for induction of cotton leaf curl disease.

Cotton leaf curl disease (CLCuD) is a major constraint to cotton production in Pakistan. Infectious clones of the monopartite begomovirus cotton leaf curl virus (CLCuV), associated with diseased cotton, are unable to induce typical symptoms in host plants. We have identified and isolated a single-stranded DNA molecule approximately 1350 nucleotides in length which, when coinoculated with the begomovirus to cotton, induces symptoms typical of CLCuD, including vein swelling, vein darkening, leaf curling, and enations. This molecule (termed DNA beta) requires the begomovirus for replication and encapsidation. The CLCuV/DNA 1/DNA beta complex, together with a similar complex previously identified in Ageratum conyzoides, represent members of an entirely new type of infectious, disease-causing agents. The implications of this finding to our understanding of the evolution of new disease-causing agents are discussed.     

Erratum to: Engineering cotton (Gossypium hirsutum L.) for resistance to cotton leaf curl disease using viral truncated AC1 DNA sequences

Virus Genes - An error notified in the labelling of Fig.&;nbsp;1b, 3′tAC1 has been erroneously published as 5′tAC1.     

Genetic variability of begomoviruses associated with cotton leaf curl disease originating from India

Summary. Cotton leaf curl disease (CLCuD) causing viruses belong to the Begomovirus genus of the family Geminiviridae. Most begomoviruses are bipartite with two molecules of circular single stranded DNA (A and B) encapsidated in icosahedral geminate particles. However, the begomoviruses associated with CLCuD have DNA- instead of DNA-B. In this communication we report the complete genomic sequence of DNA-A component of two CLCuD-causing begomoviruses, cotton leaf curl Kokhran virus-Dabawali (CLCuKV-Dab), tomato leaf curl Bangalore virus-Cotton [Fatehabad] (ToLCBV-Cotton [Fat]) and partial sequences of two other isolates cotton leaf curl Rajasthan virus-Bangalore (CLCuRV-Ban) and cotton leaf curl Kokhran virus-Ganganagar (CLCuKV-Gang). A phylogenetic analysis of these isolates along with other related begomoviruses showed that ToLCBV-Cotton [Fat] isolate was closest to the tomato leaf curl Bangalore virus-5 (ToLCBV-Ban5) where as CLCuKV-Dab isolate was close to the cotton leaf curl Kokhran virus-Faisalabad1 (CLCuKV-Fai1), cotton leaf curl Kokhran virus-72b (CLCuKV-72b) and cotton leaf curl Kokhran virus-806b (CLCuKV-806b) isolates from Pakistan. The phylogenetic analysis further showed that the ToLCBV-Cotton [Fat] and CLCuKV-Dab isolates along with CLCuKV-Fai1, CLCuKV-72b and CLCuKV-806b are closer to the ToLCBV, tomato leaf curl Gujarat virus (ToLCGV), tomato leaf curl Gujarat virus-Varanasi (ToLCGV-Var) and tomato leaf curl Sri Lanka virus (ToLCSLV) isolates, where as cotton leaf curl Alabad virus-804a (CLCuAV-804a), cotton leaf curl Multhan virus (CLCuMV) cluster with the isolates from cotton leaf curl Rajasthan virus (CLCuRV) and okra yellow vein mosaic virus (OYVMV). These results demonstrate the extensive variability observed in this group of viruses. The AC4 ORF is the least conserved among these viruses. In order to further asses the variability in the CLCuD-causing begomoviruses, the region showing minimum similarity in the DNA-A sequence was first determined by a comparison of segments of different lengths of the aligned sequences. The results indicated that region 2411–424 (771nt) was the least conserved. A phylogenetic tree constructed using the sequences of all the CLCuD causing begomoviruses, corresponding to the least conserved region showed that they form two distinct clusters.     

Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan.

Recent reports have suggested that cotton leaf curl virus (CLCuV), a geminivirus of the genus Begomovirus, may be responsible for cotton leaf curl disease in Pakistan. However, the causal agent of the disease remains unclear as CLCuV genomic components resembling begomovirus DNA A are unable to induce typical disease symptoms when reintroduced into plants. All attempts to isolate a genomic component equivalent to begomovirus DNA B have been unsuccessful. Here, we describe the isolation and characterisation of a novel circular single-stranded (ss) DNA associated with naturally infected cotton plants. In addition to a component resembling DNA A, purified geminate particles contain a smaller unrelated ssDNA that we refer to as DNA 1. DNA 1 was cloned from double-stranded replicative form of the viral DNA isolated from infected cotton plants. Blot hybridisation using probes specific for either CLCuV DNA or DNA 1 was used to demonstrate that both DNAs co-infect naturally infected cotton plants from different geographical locations. DNA 1 was detected in viruliferous Bemisia tabaci and in tobacco plants infected under laboratory conditions using B. tabaci, indicating that it is transmitted by whiteflies. Sequence analysis showed that DNA 1 is approximately half the size of CLCuV DNA but shares no homology, indicating that it is not a defective geminivirus component. DNA 1 has some homology to a genomic component of members of Nanoviridae, a family of DNA viruses that are normally transmitted by aphids or planthoppers. DNA 1 encodes a homologue of the nanovirus replication-associated protein (Rep) and has the capacity to autonomously replicate in tobacco. The data suggest that a nanovirus-like DNA has become whitefly-transmissible as a result of its association with a geminivirus and that cotton leaf curl disease may result from a mutually dependent relationship that has developed between members of two distinct DNA virus families that share a similar replication strategy.     

Replicative intermediates of Tomato leaf curl virus and its satellite DNAs

Several plant geminiviruses have been shown recently to utilize both rolling-circle replication (RCR) and recombination-dependent replication (RDR) strategies. A highly specific binding of the viral replication-associated protein (Rep) to its cognate DNA is essential for initiation of viral DNA replication and for the recognition of DNA components of the bipartite geminiviruses of the Begomovirus genus. We have extended the replication analysis to the monopartite Australian Tomato leaf curl virus (ToLCV), its Rep binding deficient mutants, and the satellite DNAs it supports. Analyses of viral DNA by two-dimensional agarose gel electrophoresis after fractionation by single-stranded (ss) DNA-selective cellulose chromatography revealed that DNA intermediates of ToLCV and its mutant were identical. Both RCR and RDR intermediates were identified. New ToLCV DNA forms were observed and characterized as subgenomic topoisomers, heterogeneous open circular double-stranded (ds) DNA, and degradation products. A 1350-nt DNA beta satellite associated with the unrelated Cotton leaf curl Multan virus (CLCuMV) was supported by ToLCV and produced intermediates of both RCR and RDR, suggesting that replication strategies of satellites are determined by the helper virus. Replicative intermediates of the 682 nt ToLCV satellite DNA could not be resolved; however, concatemers of up to octamer were detected, together with a field of hybridizing material suggestive of complementary strand replication on heterogeneous circular ssDNA templates.     

Characterization of a new begomovirus and a beta satellite associated with the leaf curl disease of French bean in northern India

Begomoviruses are emerging as serious threat to many crops throughout the world particularly in tropical and sub-tropical regions. A leaf curl disease with symptoms typical of infection by many begomoviruses was observed in French bean (Phaseolus vulgaris) at Kanpur, India, during 2010–2012. The disease caused downward leaf curling and made the plants unproductive. The disease was transmitted from infected to healthy plants through whitefly (Bemisia tabaci). The products of five samples digested with EcoRI yielded DNA fragments of about 2.7 kb. The complete sequence of the Fb1 sample comprised 2,741 nucleotides with genome organization typical of begomoviruses having two ORFs in virion-sense and five ORFs in complementary-sense separated by an intergenic region with begomovirus conserved nonanucleotide sequence, TAATATTAC. The complete DNA-A sequence homology was most closely related to Cotton leaf curl Bangalore virus with 80 % nucleotide sequence identity. Based on the demarcation criteria for identifying a begomovirus species, Fb1 is considered as a distinct begomovirus species, named French bean leaf curl virus and designated as FbLCV-[IN:Knp:12]. The complete sequence of associated satellite DNA-β comprises 1,379 nucleotides with single ORF and has 80 % identity with Papaya leaf curl beta satellite. There was no evidence of recombination in DNA-A of FbLCV and associated beta satellite DNA molecule.     

Dominance of resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) in northwestern India

Cotton leaf curl disease (CLCuD) is a major limitation to cotton production on the Indian subcontinent. A survey for viruses causing CLCuD was conducted during the 2009 and 2010 cropping seasons in the northwestern Indian cotton-growing belt in the states of Punjab, Haryana and Rajasthan. Partial sequences of 258 and full-length sequences of 22 virus genomes were determined. This study shows that the resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) is now the dominant virus in many fields. The spread and establishment of the mutant CLCuBuV in northwestern India, the variation in its genomic sequence, its virulence and infectivity, and the implications for cotton breeding are discussed.