Complete nucleotide sequence of a monopartite Begomovirus and associated satellites infecting Carica papaya in Nepal

Abstract

Carica papaya (papaya) is a fruit crop that is cultivated mostly in kitchen gardens throughout Nepal. Leaf samples of C. papaya plants with leaf curling, vein darkening, vein thickening, and a reduction in leaf size were collected from a garden in Darai village, Rampur, Nepal in 2010. Full-length clones of a monopartite Begomovirus, a betasatellite and an alphasatellite were isolated. The complete nucleotide sequence of the Begomovirus showed the arrangement of genes typical of Old World begomoviruses with the highest nucleotide sequence identity (>99 %) to an isolate of Ageratum yellow vein virus (AYVV), confirming it as an isolate of AYVV. The complete nucleotide sequence of betasatellite showed greater than 89 % nucleotide sequence identity to an isolate of Tomato leaf curl Java betasatellite originating from Indonesian. The sequence of the alphasatellite displayed 92 % nucleotide sequence identity to Sida yellow vein China alphasatellite. This is the first identification of these components in Nepal and the first time they have been identified in papaya.

Association of an Alphasatellite with Tomato Yellow Leaf Curl Virus and Ageratum Yellow Vein Virus in Japan Is Suggestive of a Recent Introduction

“…The alphasatellite identified here, SiYCCNA, has previously only been reported in Asia (China and Nepal). In Nepal the alphasatellite was in association with AYVV and ToLCJaB [23], as is the case for one of the plants examined here, and in China the satellite was associated with Kenaf leaf curl virus (FN806777), Malvastrum yellow vein Baoshan virus (FN806779) and Malvastrum yellow vein Yunnan betasatellite (FN806780). TYLCV is not normally associated with either alpha- or betasatellites.…”

“…The sequence contained all the features typical of betasatellites; a single conserved gene (known as βC1; coordinates 546-190) in the complementary-sense with the capacity to encode 118 amino acid protein, a region of sequence rich in adenine (722 to 1016) and a sequence conserved between all betasatellites (known as the satellite conserved region; 1264 to 15) that contains a predicted stem-loop structure with the nonanucleotide sequence TAATATTAC forming part of the loop. The sequence showed between 77.1% and 89% nucleotide sequence identity to isolates of Tomato leaf curl Java betasatellite (ToLCJaB) available in the databases (4 sequences available at this time) with the highest identity 89.4% to an isolate originating from Nepal isolated from papaya [23]. A phylogenetic tree, based on an alignment of the complete nucleotide sequence of the betasatellite isolated from tomato with selected betasatellite sequences available in the databases is shown in Figure 2B.…”

“…The two sequences show 99% nucleotide sequence identity and the typical arrangement of alphasatellites, containing a single large open reading frame with a coding capacity of 315 amino acids in the virion-sense (coordinates 80-1027 for both), a region of sequence rich in adenine (coordinates 1043-1236) with 51% adenine content and a predicted hairpin structure containing the nonanucleotide sequence motif TAGTATTAC, within the loop, typical of nanoviruses [24]. The two sequences showed the highest levels of nucleotide sequence identity (94.1% to 98.1%) to isolates of Sida yellow vein China alphasatellite (SiYVCNA) available in the databases (3 available at this time) with the highest levels of identity to an isolate (KC282643) originating from Nepal [23]. To all other alphasatellite sequences the levels of identity were below 88%.…”

“…The virus was first reported in Japan in 1998 [20] and is a serious constrain to tomato cultivation there [25,26]. Although AYVV is reported to cause disease of tomato in Indonesia [27], China (Guangxi province; AJ558120) and on the Okinawa Islands of Japan [23], the virus has not previously been reported on mainland Japan. In Indonesia and on Okinawa the virus is associated with Ageratum yellow vein betasatellite (AYVB) and, for Indonesian isolates, the combination AYVV with AYVB was shown experimentally to induce severe symptoms in tomato [27].…”

Association of tomato leaf curl Gujarat virus and tomato leaf curl Bangladesh betasatellite on papaya showing typical leaf curl symptoms in North India

“…A diversity study on begomoviruses associated with papaya leaf curl disease in India highlighted the rapid evolution of begomoviral host range by giving an extensive list of begomovirus species and associated satellites reported in papaya (Singh-Pant et al 2012). Presence of many begomoviruses have been reported on papaya like papaya leaf curl virus (PaLCuV) (Saxena et al 1998b), tomato leaf curl New Delhi virus (ToLCNDV) (Raj et al 2008), Papaya leaf crumple virus (Singh-Pant et al 2012) and ageratum yellow vein virus (AYVV) (Shahid et al 2013). Likewise, association of many betasatellites has also been reported in papaya leaf curl disease, e.g., papaya leaf curl betasatellite (PaLCuB), tomato leaf curl betasatellite (ToLCB), croton yellow vein mosaic betasatellite (CroYMB) (Singh-Pant et al 2012) and tomato leaf curl java betasatellite (ToLCuJB) (Shahid et al 2013).…”