Three variants of cotton leaf curl begomoviruses with their satellite molecules are associated with cotton leaf curl disease aggravation in New Delhi

Abstract

Cotton leaf curl disease (CLCuD), caused by monopartite begomoviruses and its satellite molecules, is one of the serious constrains in cultivation of cotton in India. In the present study, five CLCuD-begomovirus and its associated satellite molecules were characterized based on rolling circle amplification and sequencing of complete genome. Sequence analysis showed 82-99 % nucleotide identity among them. The phylogenetic analysis and nt identity matrix determined that of the five CLCuD-begomovirus isolates, three IARI-34, IARI-42 and IARI-50 were members of Cotton leaf curl Multan virus (CLCuMuV)-Rajasthan isolates, designated as CLCuMuV-Rajasthan-34 and two, IARI-30 and IARI-45 of Cotton leaf curl Kokhran virus (CLCuKoV)-Burewala isolates, designated as CLCuKoV-Burewala-45. The present CLCuMuVRajasthan-34 is recombinant isolate showing recombination events in IR, C1 and C4 regions of its genome with high probality (P = 9.9 9 10 -10 -3.2 9 10 -6 ). Same species of betasatellite (1371 nt) molecules obtained from both the present isolates was related with cotton leaf curl Multan betasatellite by 89-97 % nt identity. Three alphasatellites (1366-1396 nt) related to Cotton leaf curl Burewala alphasatellite and Gossypium darwinii symptomless alphasatellite by 86 % nt identity were also obtained. This is the first report of appearance of CLCuKoV-Burewala isolate and CLCuD associated alphasatellites in New Delhi. The present study demonstrated that CLCuD in New Delhi is caused by three kinds of variants, two are strains of CLCuMuV and one of CLCuKoV, either by single or mixed infection along with beta-and alphasatellite molecues.

Dominance of recombinant cotton leaf curl Multan-Rajasthan virus associated with cotton leaf curl disease outbreak in northwest India

“…The cotton leaf curl disease (CLCuD) has become a major economic constraint to cotton production in the Haryana, Punjab and Rajasthan states in northwestern (NW) India accounting for 1.1 Mha [2][3][4]. The CLCuD is caused by whitefly (Bemisiatabaci)-transmitted monopartite (~2.7 kb ssDNA-A) begomoviral species in association with betasatellite (~1.35 kb ssDNA) and alphasatellite molecules (~1.4 kb ssDNA) that results in the world's losses to the cotton [4][5][6][7]. The CLCuD associated begomovirus genome encodes the coat protein (CP; V1 ORF) and V2 protein on the virion-sense, and the replication-associated protein (Rep; C1 ORF), transcriptional activator protein (TrAP; C2 ORF), replication enhancer protein (REn; C3 ORF) and C4 protein on the complementary-sense strand [5,8].…”

“…More than nine CLCuD-begomoviruses species have been reported to be associated with the CLCuD in the Indian subcontinent [23]. The most widespread and core CLCuD-begomoviruses are Cotton leaf curl Alabad virus (CLCuAlV), Cotton leaf curl Kokhran virus (CLCuKoV), and Cotton leaf curl Multan virus (CLCuMuV) [7,21,22,24,25]. The non-core CLCuD-begomoviruses are Cotton leaf curl Bangalore virus (CLCuBaV), Cotton leaf curl Gezira virus (CLCuGeV), Okraenation leaf curl virus (OEnLCV), Papaya leaf curl virus (PaLCuV), Tomato leaf curl Bangalore virus (ToLCuBaV), Tomato leaf curl New Delhi virus (ToLCNDV), and occasionally associated with the CLCuD complex in the Indian subcontinent [21,24,26,27].…”

“…In addition, one mastrevirus, Chickpea chlorotic dwarf virus (CpCDV) has been reported in association with leaf curl symptoms in cotton in Pakistan [28]. The Cotton leaf curl Multan betasatellite (CLCuMB) is the only betasatellite species detected in association with the CLCuD complex in the Indian subcontinent [7,[21][22]25,29,30]. A number of different alphasatellites, Cotton leaf curl Multan alphasatellite (CLCuMuA), Cotton leaf curl Lucknow alphasatellite (CLCuLuA), Gossypium darwinii symptomless alphasatellite (GDarSLA) and Gossypium mustilinum symptomless alphasatellite (GMusSLA) have been reported to be associated with the CLCuD complex in this subcontinent [7,[21][22]25,29,31].…”

“…The Cotton leaf curl Multan betasatellite (CLCuMB) is the only betasatellite species detected in association with the CLCuD complex in the Indian subcontinent [7,[21][22]25,29,30]. A number of different alphasatellites, Cotton leaf curl Multan alphasatellite (CLCuMuA), Cotton leaf curl Lucknow alphasatellite (CLCuLuA), Gossypium darwinii symptomless alphasatellite (GDarSLA) and Gossypium mustilinum symptomless alphasatellite (GMusSLA) have been reported to be associated with the CLCuD complex in this subcontinent [7,[21][22]25,29,31]. The recombination phenomenon is a major driving force in the evolution of begomovirus genomes [32][33][34][35] including CLCuD-begomoviruses [7,25,36].…”

“…A number of different alphasatellites, Cotton leaf curl Multan alphasatellite (CLCuMuA), Cotton leaf curl Lucknow alphasatellite (CLCuLuA), Gossypium darwinii symptomless alphasatellite (GDarSLA) and Gossypium mustilinum symptomless alphasatellite (GMusSLA) have been reported to be associated with the CLCuD complex in this subcontinent [7,[21][22]25,29,31]. The recombination phenomenon is a major driving force in the evolution of begomovirus genomes [32][33][34][35] including CLCuD-begomoviruses [7,25,36]. The CLCuMB sequence has also been reported to be a recombinant [37] and this recombinant betasatellite has role in resistancebreaking in cotton in Pakistan [37,38].…”