Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees

Abstract

A novel circular DNA virus sequence has been identified through next-generation sequencing and in silico assembly of small RNAs of 21-24 nt from an apple tree grown in China. The virus genome was cloned using two independent approaches and sequenced. With a size of 2932 nt, it showed the same genomic structure and conserved origin of replication reported for members of the family Geminiviridae. However, the low nucleotide and amino acid sequence identity with known geminiviruses indicated that it was a novel virus, for which the provisional name apple geminivirus (AGV) is proposed. Rolling circle amplification followed by RFLP analyses indicated that AGV was a virus with a monopartite DNA genome. This result was in line with bioassays showing that the cloned viral genome was infectious in several herbaceous plants (Nicotiana bethamiana, Nicotiana glutinosa and Solanum lycopersicum), thus confirming it was complete and biologically active, although no symptoms were observed in these experimental hosts. AGV genome structure and phylogenetic analyses did not support the inclusion of this novel species in any of the established genera in the family Geminiviridae. A survey of 165 apple trees grown in four Chinese provinces showed a prevalence of 7.2 % for AGV, confirming its presence in several cultivars and geographical areas in China, although no obvious relationship between virus infection and specific symptoms was found.

Capulavirus and Grablovirus: two new genera in the family Geminiviridae

“…KM386645) [20] and thirteen GGVA complete genomes isolated from grapevine in China (KX570611), Hungary (KX570618), Israel (KX618694), Japan (KX570610, KX570612, KX570613, KX570615, KX570616, KX570617) and South Korea (KX570607, KX570609, KX570614) group together, with 94% bootstrap support (Fig. 2).…”

“…Analyses of these sequences (pairwise identities and phylogenetics), coupled with the identification of insect vectors and particle morphology, have allowed us to determine with great confidence that some of these divergent viruses should be classified as members of two new genera in the family Geminiviridae, which was approved by the Executive Committee of the ICTV: 1) Capulavirus, which will for now include four species, Alfalfa leaf curl virus, Euphorbia caputmedusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus [5,6,30,36] 2) Grablovirus, which will for now include one species, Grapevine red blotch virus [18,28,35] In addition, two other species of highly divergent viruses that are closely related to geminiviruses have been accepted by the Executive Committee of the ICTV for inclusion in the family Geminiviridae and will remain unassigned to a genus, awaiting identification of the vector species and confirmation of particle morphology. These new species are: 1) Citrus chlorotic dwarf associated virus [17,21] 2) Mulberry mosaic dwarf associated virus [23,24] Furthermore, recently, a single virus isolated from an apple tree in China (tentatively referred to as apple geminivirus; AGmV) [20] and 13 virus isolates from grapevine in Hungary, Israel, Japan and South Korea (tentatively referred to as grapevine geminivirus A; GGVA) sharing [97% pairwise identity have been discovered [2]. These have distinctly geminivirus-like genome organisations and are more closely related to members of some established geminivirus species than they are to citrus chlorotic dwarf associated virus (CCDaV) and mulberry mosaic dwarf associated virus (MMCaV).…”

Molecular Characterization and Genomic Function of Grapevine Geminivirus A

“…Geminiviruses usually infect herbaceous plants, however, following the development of high throughput sequencing, more geminiviruses have been identified from woody plants. Citrus chlorotic dwarf-associated virus (CCDaV) ( Loconsole et al, 2012 ), GRBV ( Al Rwahnih et al, 2013 ), jatropha curcas mosaic virus (JaMV) ( Wang et al, 2014 ), mulberry mosaic dwarf-associated virus (MMDaV) ( Ma et al, 2015 ), and apple geminivirus (AGV) ( Liang et al, 2015 ) have been reported. GGVA, which was recently discovered from two table grape cultivars from Korea, is a tentative species belonging to the family Geminiviridae ( Al Rwahnih et al, 2017 ).…”

The ever increasing diversity of begomoviruses infecting non‐cultivated hosts: new species from Sida spp. and Leonurus sibiricus, plus two New World alphasatellites

“…No functional domains were predicted in the AV2-like protein. BLASTp analysis with the CP and AV2 proteins detected only a very low similarity with a highly divergent monopartite geminivirus recently described in China infecting apple trees, named 'apple geminivirus' (AGV) (Liang et al, 2015). The BR:Sab889:10 CP shares 27% amino acid (aa) identity (90% coverage, E value 2e −12 ) with the AGV CP and the AV2-like protein shares 43% aa identity (83% coverage, E value 1e −15 ) with the putative V2 protein of AGV.…”